https://launchpad.net/ubuntu/+source/apbs/1.5+dfsg1-3/+build/19276035 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-020 4.4.0-178-generic #208-Ubuntu SMP Sun Apr 5 23:44:42 UTC 2020 s390x Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.9 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 8 May 04:31:31 ntpdate[1844]: adjust time server 10.211.37.1 offset -0.000089 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19276035 --image-type chroot /home/buildd/filecache-default/0c27a67c210d6cb13869ddd14c37f7dc742e8ea2 Creating target for build PACKAGEBUILD-19276035 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19276035 Starting target for build PACKAGEBUILD-19276035 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19276035 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19276035 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19276035 Updating target for build PACKAGEBUILD-19276035 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main s390x Packages [922 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [506 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe s390x Packages [8308 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5170 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x Packages [76.4 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [43.4 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe s390x Packages [423 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [295 kB] Fetched 16.3 MB in 3s (5340 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files cpp-9 dash debconf e2fsprogs g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv libacl1 libapt-pkg6.0 libasan5 libatomic1 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libext2fs2 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libitm1 libncurses6 libncursesw6 libperl5.30 libprocps8 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 linux-libc-dev logsave make ncurses-base ncurses-bin perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata 56 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 41.7 MB of archives. After this operation, 159 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libcrypt-dev s390x 1:4.4.15-1ubuntu1 [107 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libcrypt1 s390x 1:4.4.15-1ubuntu1 [80.7 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main s390x base-files s390x 11ubuntu7 [60.0 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libperl5.30 s390x 5.30.0-10 [3781 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x perl s390x 5.30.0-10 [224 kB] Get:6 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x perl-base s390x 5.30.0-10 [1422 kB] Get:7 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x perl-modules-5.30 all 5.30.0-10 [2738 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main s390x debconf all 1.5.74 [121 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main s390x dash s390x 0.5.10.2-7 [86.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main s390x ncurses-bin s390x 6.2-1 [170 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main s390x ncurses-base all 6.2-1 [18.7 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main s390x sysvinit-utils s390x 2.96-3ubuntu1 [20.6 kB] Get:13 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libubsan1 s390x 10.1.0-1ubuntu1 [155 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libitm1 s390x 10.1.0-1ubuntu1 [28.6 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libgomp1 s390x 10.1.0-1ubuntu1 [114 kB] Get:16 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gcc-10-base s390x 10.1.0-1ubuntu1 [19.3 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libgcc-s1 s390x 10.1.0-1ubuntu1 [30.4 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libcc1-0 s390x 10.1.0-1ubuntu1 [39.3 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libatomic1 s390x 10.1.0-1ubuntu1 [8388 B] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libstdc++6 s390x 10.1.0-1ubuntu1 [518 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main s390x systemd-sysv s390x 245.5-2ubuntu1 [10.3 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main s390x systemd-timesyncd s390x 245.5-2ubuntu1 [26.0 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main s390x libacl1 s390x 2.2.53-8 [18.5 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main s390x libcap2 s390x 1:2.33-1 [17.7 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main s390x libcryptsetup12 s390x 2:2.3.1-1ubuntu1 [169 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main s390x libidn2-0 s390x 2.3.0-1 [51.7 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main s390x systemd s390x 245.5-2ubuntu1 [3430 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main s390x libsystemd0 s390x 245.5-2ubuntu1 [249 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main s390x libudev1 s390x 245.5-2ubuntu1 [73.1 kB] Get:30 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libapt-pkg6.0 s390x 2.1.0 [779 kB] Get:31 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gpgv s390x 2.2.20-1ubuntu1 [186 kB] Get:32 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x apt s390x 2.1.0 [1249 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main s390x logsave s390x 1.45.6-1ubuntu1 [10.1 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main s390x libext2fs2 s390x 1.45.6-1ubuntu1 [178 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main s390x e2fsprogs s390x 1.45.6-1ubuntu1 [508 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main s390x libncurses6 s390x 6.2-1 [94.9 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main s390x libncursesw6 s390x 6.2-1 [122 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main s390x libtinfo6 s390x 6.2-1 [84.6 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main s390x libcom-err2 s390x 1.45.6-1ubuntu1 [9512 B] Get:40 http://ftpmaster.internal/ubuntu groovy/main s390x libprocps8 s390x 2:3.3.16-4ubuntu1 [30.9 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main s390x libss2 s390x 1.45.6-1ubuntu1 [11.0 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main s390x procps s390x 2:3.3.16-4ubuntu1 [225 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main s390x libsqlite3-0 s390x 3.31.1-5 [512 kB] Get:44 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x tzdata all 2020a-0ubuntu1 [293 kB] Get:45 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libasan5 s390x 9.3.0-12ubuntu1 [361 kB] Get:46 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x g++-9 s390x 9.3.0-12ubuntu1 [6609 kB] Get:47 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gcc-9 s390x 9.3.0-12ubuntu1 [6472 kB] Get:48 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libstdc++-9-dev s390x 9.3.0-12ubuntu1 [1678 kB] Get:49 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libgcc-9-dev s390x 9.3.0-12ubuntu1 [704 kB] Get:50 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x cpp-9 s390x 9.3.0-12ubuntu1 [5731 kB] Get:51 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gcc-9-base s390x 9.3.0-12ubuntu1 [19.5 kB] Get:52 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gpg s390x 2.2.20-1ubuntu1 [448 kB] Get:53 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gpgconf s390x 2.2.20-1ubuntu1 [119 kB] Get:54 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gpg-agent s390x 2.2.20-1ubuntu1 [218 kB] Get:55 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x linux-libc-dev s390x 5.4.0-29.33 [1098 kB] Get:56 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x make s390x 4.2.1-2 [160 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.7 MB in 1s (62.3 MB/s) (Reading database ... 12607 files and directories currently installed.) 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Unpacking libgcc-9-dev:s390x (9.3.0-12ubuntu1) over (9.3.0-10ubuntu2) ... Preparing to unpack .../11-cpp-9_9.3.0-12ubuntu1_s390x.deb ... Unpacking cpp-9 (9.3.0-12ubuntu1) over (9.3.0-10ubuntu2) ... Preparing to unpack .../12-gcc-9-base_9.3.0-12ubuntu1_s390x.deb ... Unpacking gcc-9-base:s390x (9.3.0-12ubuntu1) over (9.3.0-10ubuntu2) ... Preparing to unpack .../13-gpg_2.2.20-1ubuntu1_s390x.deb ... Unpacking gpg (2.2.20-1ubuntu1) over (2.2.19-3ubuntu2) ... Preparing to unpack .../14-gpgconf_2.2.20-1ubuntu1_s390x.deb ... Unpacking gpgconf (2.2.20-1ubuntu1) over (2.2.19-3ubuntu2) ... Preparing to unpack .../15-gpg-agent_2.2.20-1ubuntu1_s390x.deb ... Unpacking gpg-agent (2.2.20-1ubuntu1) over (2.2.19-3ubuntu2) ... Preparing to unpack .../16-linux-libc-dev_5.4.0-29.33_s390x.deb ... Unpacking linux-libc-dev:s390x (5.4.0-29.33) over (5.4.0-26.30) ... Preparing to unpack .../17-make_4.2.1-2_s390x.deb ... Unpacking make (4.2.1-2) over (4.2.1-1.2) ... Setting up perl-modules-5.30 (5.30.0-10) ... Setting up libsqlite3-0:s390x (3.31.1-5) ... Setting up linux-libc-dev:s390x (5.4.0-29.33) ... Setting up libcom-err2:s390x (1.45.6-1ubuntu1) ... Setting up libgomp1:s390x (10.1.0-1ubuntu1) ... Setting up libcap2:s390x (1:2.33-1) ... Setting up tzdata (2020a-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri May 8 04:31:45 UTC 2020. Universal Time is now: Fri May 8 04:31:45 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.2.1-2) ... Setting up libncurses6:s390x (6.2-1) ... Setting up libatomic1:s390x (10.1.0-1ubuntu1) ... Setting up libss2:s390x (1.45.6-1ubuntu1) ... Setting up libncursesw6:s390x (6.2-1) ... Setting up logsave (1.45.6-1ubuntu1) ... Setting up libubsan1:s390x (10.1.0-1ubuntu1) ... Setting up libcrypt-dev:s390x (1:4.4.15-1ubuntu1) ... Setting up gpgconf (2.2.20-1ubuntu1) ... Setting up libperl5.30:s390x (5.30.0-10) ... Setting up libcryptsetup12:s390x (2:2.3.1-1ubuntu1) ... Setting up libcc1-0:s390x (10.1.0-1ubuntu1) ... Setting up gpg (2.2.20-1ubuntu1) ... Setting up libprocps8:s390x (2:3.3.16-4ubuntu1) ... Setting up libitm1:s390x (10.1.0-1ubuntu1) ... Setting up gcc-9-base:s390x (9.3.0-12ubuntu1) ... Setting up gpg-agent (2.2.20-1ubuntu1) ... Setting up e2fsprogs (1.45.6-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libasan5:s390x (9.3.0-12ubuntu1) ... Setting up perl (5.30.0-10) ... Setting up procps (2:3.3.16-4ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Removing obsolete conffile /etc/sysctl.d/10-link-restrictions.conf ... Setting up cpp-9 (9.3.0-12ubuntu1) ... Setting up libgcc-9-dev:s390x (9.3.0-12ubuntu1) ... Setting up gcc-9 (9.3.0-12ubuntu1) ... Setting up libstdc++-9-dev:s390x (9.3.0-12ubuntu1) ... Setting up g++-9 (9.3.0-12ubuntu1) ... Setting up systemd-timesyncd (245.5-2ubuntu1) ... Setting up systemd (245.5-2ubuntu1) ... Initializing machine ID from random generator. Setting up systemd-sysv (245.5-2ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19276035 s390x groovy-proposed -c chroot:build-PACKAGEBUILD-19276035 --arch=s390x --dist=groovy-proposed --nolog apbs_1.5+dfsg1-3.dsc Initiating build PACKAGEBUILD-19276035 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-178-generic #208-Ubuntu SMP Sun Apr 5 23:44:42 UTC 2020 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-020.buildd +==============================================================================+ | apbs 1.5+dfsg1-3 (s390x) 08 May 2020 04:31 | +==============================================================================+ Package: apbs Version: 1.5+dfsg1-3 Source Version: 1.5+dfsg1-3 Distribution: groovy-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/apbs-Hs9IQ6/apbs-1.5+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-Hs9IQ6' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19276035/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- apbs_1.5+dfsg1-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-WM6o9g/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-WM6o9g/apt_archive ./ InRelease Get:2 copy:/<>/resolver-WM6o9g/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-WM6o9g/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-WM6o9g/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-WM6o9g/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 860 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-WM6o9g/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [860 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 860 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12607 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: cmake, debhelper-compat (= 12), dh-python, libmaloc-dev, mpi-default-dev, python3, python3-dev, python3-setuptools, swig, zlib1g-dev Filtered Build-Depends: cmake, debhelper-compat (= 12), dh-python, libmaloc-dev, mpi-default-dev, python3, python3-dev, python3-setuptools, swig, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-apbs-dummy' in '/<>/resolver-vGBjeW/apt_archive/sbuild-build-depends-apbs-dummy.deb'. Ign:1 copy:/<>/resolver-vGBjeW/apt_archive ./ InRelease Get:2 copy:/<>/resolver-vGBjeW/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-vGBjeW/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-vGBjeW/apt_archive ./ Sources [265 B] Get:5 copy:/<>/resolver-vGBjeW/apt_archive ./ Packages [587 B] Fetched 2971 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install apbs build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data cpp-8 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gcc-8 gcc-8-base gettext gettext-base gfortran-8 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbrotli1 libbsd0 libcbor0.6 libcroco3 libcurl4 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfido2-1 libfile-stripnondeterminism-perl libgcc-8-dev libgfortran-8-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhwloc-dev libhwloc-plugins libhwloc15 libhx509-5-heimdal libibverbs-dev libibverbs1 libicu66 libjs-jquery libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libmpdec2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpsl5 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libuv1 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mime-support mpi-default-dev node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.8 python3.8-dev python3.8-minimal swig swig4.0 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build gcc-8-locales dh-make gcc-8-multilib gcc-8-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-8-multilib gfortran-8-doc libcoarrays-dev groff lrzip krb5-doc krb5-user libtool-doc openmpi-doc pciutils gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc python3.8-venv python3.8-doc binfmt-support swig-doc swig-examples swig4.0-examples swig4.0-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data cpp-8 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gcc-8 gcc-8-base gettext gettext-base gfortran-8 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbrotli1 libbsd0 libcbor0.6 libcroco3 libcurl4 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfido2-1 libfile-stripnondeterminism-perl libgcc-8-dev libgfortran-8-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhwloc-dev libhwloc-plugins libhwloc15 libhx509-5-heimdal libibverbs-dev libibverbs1 libicu66 libjs-jquery libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libmpdec2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpsl5 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libuv1 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mime-support mpi-default-dev node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.8 python3.8-dev python3.8-minimal sbuild-build-depends-apbs-dummy swig swig4.0 zlib1g-dev 0 upgraded, 138 newly installed, 0 to remove and 0 not upgraded. Need to get 68.3 MB of archives. After this operation, 284 MB of additional disk space will be used. Get:1 copy:/<>/resolver-vGBjeW/apt_archive ./ sbuild-build-depends-apbs-dummy 0.invalid.0 [920 B] Get:2 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libpython3.8-minimal s390x 3.8.2-1ubuntu1.1 [702 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main s390x libexpat1 s390x 2.2.9-1build1 [69.8 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x python3.8-minimal s390x 3.8.2-1ubuntu1.1 [1746 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main s390x python3-minimal s390x 3.8.2-0ubuntu2 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main s390x mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main s390x libmpdec2 s390x 2.4.2-3 [82.4 kB] Get:8 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libpython3.8-stdlib s390x 3.8.2-1ubuntu1.1 [1626 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x python3.8 s390x 3.8.2-1ubuntu1.1 [364 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main s390x libpython3-stdlib s390x 3.8.2-0ubuntu2 [7068 B] Get:11 http://ftpmaster.internal/ubuntu groovy/main s390x python3 s390x 3.8.2-0ubuntu2 [47.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main s390x libbsd0 s390x 0.10.0-1 [43.7 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main s390x bsdmainutils s390x 11.1.2ubuntu3 [181 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main s390x libuchardet0 s390x 0.0.6-3build1 [64.6 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main s390x groff-base s390x 1.22.4-5 [812 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main s390x libpipeline1 s390x 1.5.2-2build1 [26.5 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main s390x man-db s390x 2.9.1-1 [1101 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main s390x libmagic-mgc s390x 1:5.38-4 [219 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main s390x libmagic1 s390x 1:5.38-4 [72.8 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main s390x file s390x 1:5.38-4 [23.1 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main s390x libelf1 s390x 0.176-1.1build1 [47.5 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main s390x libglib2.0-0 s390x 2.64.2-1 [1180 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main s390x libicu66 s390x 66.1-2ubuntu2 [8263 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main s390x libxml2 s390x 2.9.10+dfsg-5 [659 kB] Get:25 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x python3-pkg-resources all 46.1.3-1 [127 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main s390x gettext-base s390x 0.19.8.1-10build1 [49.0 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main s390x libcbor0.6 s390x 0.6.0-0ubuntu1 [21.7 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main s390x libedit2 s390x 3.1-20191231-1 [82.5 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main s390x libfido2-1 s390x 1.3.1-1ubuntu2 [42.8 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main s390x libkrb5support0 s390x 1.17-6ubuntu4 [30.2 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main s390x libk5crypto3 s390x 1.17-6ubuntu4 [78.1 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main s390x libkeyutils1 s390x 1.6.1-2ubuntu1 [9796 B] Get:33 http://ftpmaster.internal/ubuntu groovy/main s390x libkrb5-3 s390x 1.17-6ubuntu4 [310 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main s390x libgssapi-krb5-2 s390x 1.17-6ubuntu4 [111 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main s390x libnuma1 s390x 2.0.12-1 [20.3 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main s390x libpsl5 s390x 0.21.0-1ubuntu1 [51.4 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main s390x libuv1 s390x 1.35.0-2ubuntu1 [75.1 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main s390x libxau6 s390x 1:1.0.9-0ubuntu1 [7212 B] Get:39 http://ftpmaster.internal/ubuntu groovy/main s390x libxdmcp6 s390x 1:1.1.3-0ubuntu1 [10.4 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main s390x libxcb1 s390x 1.14-2 [42.3 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main s390x libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main s390x libx11-6 s390x 2:1.6.9-2ubuntu1 [550 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main s390x libxext6 s390x 2:1.3.4-0ubuntu1 [27.0 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main s390x openssh-client s390x 1:8.2p1-4 [633 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main s390x libsigsegv2 s390x 2.12-2 [13.8 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main s390x m4 s390x 1.4.18-4 [196 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main s390x autoconf all 2.69-11.1 [321 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main s390x automake all 1:1.16.1-4ubuntu6 [522 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main s390x autopoint all 0.19.8.1-10build1 [412 kB] Get:51 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x cmake-data all 3.16.3-2ubuntu1 [1612 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main s390x libarchive13 s390x 3.4.0-2ubuntu1 [310 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main s390x libbrotli1 s390x 1.0.7-6.1 [260 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main s390x libroken18-heimdal s390x 7.7.0+dfsg-1ubuntu1 [40.0 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main s390x libasn1-8-heimdal s390x 7.7.0+dfsg-1ubuntu1 [148 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main s390x libheimbase1-heimdal s390x 7.7.0+dfsg-1ubuntu1 [27.8 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main s390x libhcrypto4-heimdal s390x 7.7.0+dfsg-1ubuntu1 [83.3 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main s390x libwind0-heimdal s390x 7.7.0+dfsg-1ubuntu1 [47.7 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main s390x libhx509-5-heimdal s390x 7.7.0+dfsg-1ubuntu1 [98.3 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main s390x libkrb5-26-heimdal s390x 7.7.0+dfsg-1ubuntu1 [191 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main s390x libheimntlm0-heimdal s390x 7.7.0+dfsg-1ubuntu1 [14.5 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main s390x libgssapi3-heimdal s390x 7.7.0+dfsg-1ubuntu1 [87.2 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main s390x libsasl2-modules-db s390x 2.1.27+dfsg-2 [14.6 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main s390x libsasl2-2 s390x 2.1.27+dfsg-2 [47.7 kB] Get:65 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libldap-common all 2.4.49+dfsg-2ubuntu2 [17.4 kB] Get:66 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libldap-2.4-2 s390x 2.4.49+dfsg-2ubuntu2 [146 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main s390x libnghttp2-14 s390x 1.40.0-1build1 [74.2 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build1 [50.9 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main s390x libssh-4 s390x 0.9.3-2ubuntu2 [154 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main s390x libcurl4 s390x 7.68.0-1ubuntu2 [218 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main s390x libjsoncpp1 s390x 1.7.4-3.1ubuntu2 [69.6 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main s390x librhash0 s390x 1.3.9-1 [112 kB] Get:73 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x cmake s390x 3.16.3-2ubuntu1 [3073 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/universe s390x gcc-8-base s390x 8.4.0-3ubuntu2 [18.7 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/universe s390x cpp-8 s390x 8.4.0-3ubuntu2 [6906 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/universe s390x libgcc-8-dev s390x 8.4.0-3ubuntu2 [654 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/universe s390x gcc-8 s390x 8.4.0-3ubuntu2 [7761 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main s390x libtool all 2.4.6-14 [161 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main s390x dh-autoreconf all 19 [16.1 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main s390x libdebhelper-perl all 13ubuntu1 [62.5 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:83 http://ftpmaster.internal/ubuntu groovy/main s390x libfile-stripnondeterminism-perl all 1.8.0-1 [16.2 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main s390x dh-strip-nondeterminism all 1.8.0-1 [5228 B] Get:85 http://ftpmaster.internal/ubuntu groovy/main s390x dwz s390x 0.13-5 [146 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main s390x libcroco3 s390x 0.6.13-1 [73.7 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main s390x gettext s390x 0.19.8.1-10build1 [867 kB] Get:88 http://ftpmaster.internal/ubuntu groovy/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/main s390x po-debconf all 1.0.21 [233 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/main s390x debhelper all 13ubuntu1 [877 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main s390x python3-lib2to3 all 3.8.2-1ubuntu1 [74.1 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/main s390x python3-distutils all 3.8.2-1ubuntu1 [140 kB] Get:93 http://ftpmaster.internal/ubuntu groovy-proposed/universe s390x dh-python all 4.20200315 [85.8 kB] Get:94 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libgfortran5 s390x 10.1.0-1ubuntu1 [415 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/universe s390x libgfortran-8-dev s390x 8.4.0-3ubuntu2 [347 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/universe s390x gfortran-8 s390x 8.4.0-3ubuntu2 [7378 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-3-200 s390x 3.4.0-1 [50.3 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-route-3-200 s390x 3.4.0-1 [137 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main s390x libibverbs1 s390x 28.0-1ubuntu1 [51.1 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/main s390x ibverbs-providers s390x 28.0-1ubuntu1 [221 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-2.1-7 s390x 2.1.11-stable-1 [126 kB] Get:102 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-core-2.1-7 s390x 2.1.11-stable-1 [82.5 kB] Get:103 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-extra-2.1-7 s390x 2.1.11-stable-1 [54.6 kB] Get:104 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-pthreads-2.1-7 s390x 2.1.11-stable-1 [7184 B] Get:105 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-openssl-2.1-7 s390x 2.1.11-stable-1 [13.5 kB] Get:106 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-dev s390x 2.1.11-stable-1 [251 kB] Get:107 http://ftpmaster.internal/ubuntu groovy/main s390x libexpat1-dev s390x 2.2.9-1build1 [112 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/universe s390x libhwloc15 s390x 2.2.0+dfsg-3 [117 kB] Get:109 http://ftpmaster.internal/ubuntu groovy-proposed/universe s390x node-jquery all 3.5.1+dfsg-3 [309 kB] Get:110 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libjs-jquery all 3.5.1+dfsg-3 [2308 B] Get:111 http://ftpmaster.internal/ubuntu groovy/main s390x libltdl7 s390x 2.4.6-14 [38.2 kB] Get:112 http://ftpmaster.internal/ubuntu groovy/main s390x libltdl-dev s390x 2.4.6-14 [162 kB] Get:113 http://ftpmaster.internal/ubuntu groovy/universe s390x libmaloc1 s390x 1.5-1 [84.7 kB] Get:114 http://ftpmaster.internal/ubuntu groovy/universe s390x libmaloc-dev s390x 1.5-1 [104 kB] Get:115 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-3-dev s390x 3.4.0-1 [89.9 kB] Get:116 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-route-3-dev s390x 3.4.0-1 [155 kB] Get:117 http://ftpmaster.internal/ubuntu groovy/main s390x libpciaccess0 s390x 0.16-0ubuntu1 [16.5 kB] Get:118 http://ftpmaster.internal/ubuntu groovy/main s390x libxnvctrl0 s390x 440.64-0ubuntu1 [11.1 kB] Get:119 http://ftpmaster.internal/ubuntu groovy/main s390x ocl-icd-libopencl1 s390x 2.2.11-1ubuntu1 [31.0 kB] Get:120 http://ftpmaster.internal/ubuntu groovy/universe s390x libhwloc-plugins s390x 2.2.0+dfsg-3 [13.9 kB] Get:121 http://ftpmaster.internal/ubuntu groovy/universe s390x libpmix2 s390x 3.1.5-1 [428 kB] Get:122 http://ftpmaster.internal/ubuntu groovy/universe s390x libopenmpi3 s390x 4.0.3-6ubuntu1 [1821 kB] Get:123 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libpython3.8 s390x 3.8.2-1ubuntu1.1 [1662 kB] Get:124 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libpython3.8-dev s390x 3.8.2-1ubuntu1.1 [3852 kB] Get:125 http://ftpmaster.internal/ubuntu groovy/main s390x libpython3-dev s390x 3.8.2-0ubuntu2 [7232 B] Get:126 http://ftpmaster.internal/ubuntu groovy/universe s390x openmpi-common all 4.0.3-6ubuntu1 [151 kB] Get:127 http://ftpmaster.internal/ubuntu groovy/universe s390x openmpi-bin s390x 4.0.3-6ubuntu1 [66.0 kB] Get:128 http://ftpmaster.internal/ubuntu groovy/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-2ubuntu1 [166 kB] Get:129 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x python3.8-dev s390x 3.8.2-1ubuntu1.1 [514 kB] Get:130 http://ftpmaster.internal/ubuntu groovy/main s390x python3-dev s390x 3.8.2-0ubuntu2 [1212 B] Get:131 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x python3-setuptools all 46.1.3-1 [325 kB] Get:132 http://ftpmaster.internal/ubuntu groovy/universe s390x swig4.0 s390x 4.0.1-5build1 [994 kB] Get:133 http://ftpmaster.internal/ubuntu groovy/universe s390x swig all 4.0.1-5build1 [5528 B] Get:134 http://ftpmaster.internal/ubuntu groovy/main s390x libnuma-dev s390x 2.0.12-1 [32.0 kB] Get:135 http://ftpmaster.internal/ubuntu groovy/universe s390x libhwloc-dev s390x 2.2.0+dfsg-3 [189 kB] Get:136 http://ftpmaster.internal/ubuntu groovy/main s390x libibverbs-dev s390x 28.0-1ubuntu1 [438 kB] Get:137 http://ftpmaster.internal/ubuntu groovy/universe s390x libopenmpi-dev s390x 4.0.3-6ubuntu1 [813 kB] Get:138 http://ftpmaster.internal/ubuntu groovy/universe s390x mpi-default-dev s390x 1.13 [3748 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.3 MB in 1s (51.7 MB/s) Selecting previously unselected package libpython3.8-minimal:s390x. (Reading database ... 12607 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.2-1ubuntu1.1_s390x.deb ... Unpacking libpython3.8-minimal:s390x (3.8.2-1ubuntu1.1) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../libexpat1_2.2.9-1build1_s390x.deb ... Unpacking libexpat1:s390x (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2-1ubuntu1.1_s390x.deb ... Unpacking python3.8-minimal (3.8.2-1ubuntu1.1) ... Setting up libpython3.8-minimal:s390x (3.8.2-1ubuntu1.1) ... Setting up libexpat1:s390x (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.2-1ubuntu1.1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12898 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_s390x.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... 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Selecting previously unselected package libicu66:s390x. Preparing to unpack .../012-libicu66_66.1-2ubuntu2_s390x.deb ... Unpacking libicu66:s390x (66.1-2ubuntu2) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../013-libxml2_2.9.10+dfsg-5_s390x.deb ... Unpacking libxml2:s390x (2.9.10+dfsg-5) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../014-python3-pkg-resources_46.1.3-1_all.deb ... Unpacking python3-pkg-resources (46.1.3-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../015-gettext-base_0.19.8.1-10build1_s390x.deb ... Unpacking gettext-base (0.19.8.1-10build1) ... Selecting previously unselected package libcbor0.6:s390x. Preparing to unpack .../016-libcbor0.6_0.6.0-0ubuntu1_s390x.deb ... Unpacking libcbor0.6:s390x (0.6.0-0ubuntu1) ... Selecting previously unselected package libedit2:s390x. Preparing to unpack .../017-libedit2_3.1-20191231-1_s390x.deb ... Unpacking libedit2:s390x (3.1-20191231-1) ... Selecting previously unselected package libfido2-1:s390x. Preparing to unpack .../018-libfido2-1_1.3.1-1ubuntu2_s390x.deb ... Unpacking libfido2-1:s390x (1.3.1-1ubuntu2) ... Selecting previously unselected package libkrb5support0:s390x. Preparing to unpack .../019-libkrb5support0_1.17-6ubuntu4_s390x.deb ... Unpacking libkrb5support0:s390x (1.17-6ubuntu4) ... Selecting previously unselected package libk5crypto3:s390x. Preparing to unpack .../020-libk5crypto3_1.17-6ubuntu4_s390x.deb ... Unpacking libk5crypto3:s390x (1.17-6ubuntu4) ... Selecting previously unselected package libkeyutils1:s390x. Preparing to unpack .../021-libkeyutils1_1.6.1-2ubuntu1_s390x.deb ... Unpacking libkeyutils1:s390x (1.6.1-2ubuntu1) ... Selecting previously unselected package libkrb5-3:s390x. Preparing to unpack .../022-libkrb5-3_1.17-6ubuntu4_s390x.deb ... Unpacking libkrb5-3:s390x (1.17-6ubuntu4) ... Selecting previously unselected package libgssapi-krb5-2:s390x. 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Selecting previously unselected package libnghttp2-14:s390x. Preparing to unpack .../056-libnghttp2-14_1.40.0-1build1_s390x.deb ... Unpacking libnghttp2-14:s390x (1.40.0-1build1) ... Selecting previously unselected package librtmp1:s390x. Preparing to unpack .../057-librtmp1_2.4+20151223.gitfa8646d.1-2build1_s390x.deb ... Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build1) ... Selecting previously unselected package libssh-4:s390x. Preparing to unpack .../058-libssh-4_0.9.3-2ubuntu2_s390x.deb ... Unpacking libssh-4:s390x (0.9.3-2ubuntu2) ... Selecting previously unselected package libcurl4:s390x. Preparing to unpack .../059-libcurl4_7.68.0-1ubuntu2_s390x.deb ... Unpacking libcurl4:s390x (7.68.0-1ubuntu2) ... Selecting previously unselected package libjsoncpp1:s390x. Preparing to unpack .../060-libjsoncpp1_1.7.4-3.1ubuntu2_s390x.deb ... Unpacking libjsoncpp1:s390x (1.7.4-3.1ubuntu2) ... Selecting previously unselected package librhash0:s390x. 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Setting up libpipeline1:s390x (1.5.2-2build1) ... Setting up libpciaccess0:s390x (0.16-0ubuntu1) ... Setting up libxau6:s390x (1:1.0.9-0ubuntu1) ... Setting up libkeyutils1:s390x (1.6.1-2ubuntu1) ... Setting up libpsl5:s390x (0.21.0-1ubuntu1) ... Setting up mime-support (3.64ubuntu1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:s390x (2.64.2-1) ... No schema files found: doing nothing. Setting up libicu66:s390x (66.1-2ubuntu2) ... Setting up libdebhelper-perl (13ubuntu1) ... Setting up libbrotli1:s390x (1.0.7-6.1) ... Setting up libnghttp2-14:s390x (1.40.0-1build1) ... Setting up libmagic1:s390x (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-4) ... Setting up libcbor0.6:s390x (0.6.0-0ubuntu1) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu2) ... Setting up libkrb5support0:s390x (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:s390x (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:s390x (1.35.0-2ubuntu1) ... Setting up libexpat1-dev:s390x (2.2.9-1build1) ... Setting up libx11-data (2:1.6.9-2ubuntu1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libsigsegv2:s390x (2.12-2) ... Setting up libhwloc15:s390x (2.2.0+dfsg-3) ... Setting up libevent-core-2.1-7:s390x (2.1.11-stable-1) ... Setting up libevent-2.1-7:s390x (2.1.11-stable-1) ... Setting up gcc-8-base:s390x (8.4.0-3ubuntu2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libk5crypto3:s390x (1.17-6ubuntu4) ... Setting up libltdl7:s390x (2.4.6-14) ... Setting up libgcc-8-dev:s390x (8.4.0-3ubuntu2) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-2) ... Setting up libgfortran5:s390x (10.1.0-1ubuntu1) ... Setting up libroken18-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-2ubuntu1) ... Setting up libnuma1:s390x (2.0.12-1) ... Setting up ocl-icd-libopencl1:s390x (2.2.11-1ubuntu1) ... Setting up librhash0:s390x (1.3.9-1) ... Setting up libuchardet0:s390x (0.0.6-3build1) ... Setting up libnl-3-200:s390x (3.4.0-1) ... Setting up openmpi-common (4.0.3-6ubuntu1) ... Setting up libsub-override-perl (0.09-2) ... Setting up cmake-data (3.16.3-2ubuntu1) ... Setting up libkrb5-3:s390x (1.17-6ubuntu4) ... Setting up libmpdec2:s390x (2.4.2-3) ... Setting up cpp-8 (8.4.0-3ubuntu2) ... Setting up swig4.0 (4.0.1-5build1) ... Setting up libpython3.8-stdlib:s390x (3.8.2-1ubuntu1.1) ... Setting up libfido2-1:s390x (1.3.1-1ubuntu2) ... Setting up python3.8 (3.8.2-1ubuntu1.1) ... Setting up libbsd0:s390x (0.10.0-1) ... Setting up libelf1:s390x (0.176-1.1build1) ... Setting up libxml2:s390x (2.9.10+dfsg-5) ... Setting up node-jquery (3.5.1+dfsg-3) ... Setting up libjsoncpp1:s390x (1.7.4-3.1ubuntu2) ... Setting up libpython3-stdlib:s390x (3.8.2-0ubuntu2) ... Setting up libheimbase1-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up libevent-pthreads-2.1-7:s390x (2.1.11-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libgfortran-8-dev:s390x (8.4.0-3ubuntu2) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu1) ... Setting up libevent-extra-2.1-7:s390x (2.1.11-stable-1) ... Setting up libxcb1:s390x (1.14-2) ... Setting up gcc-8 (8.4.0-3ubuntu2) ... Setting up swig (4.0.1-5build1) ... Setting up libtool (2.4.6-14) ... Setting up libarchive13:s390x (3.4.0-2ubuntu1) ... Setting up gfortran-8 (8.4.0-3ubuntu2) ... Setting up libasn1-8-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up libedit2:s390x (3.1-20191231-1) ... Setting up libevent-openssl-2.1-7:s390x (2.1.11-stable-1) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up libhcrypto4-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up libnuma-dev:s390x (2.0.12-1) ... Setting up libnl-route-3-200:s390x (3.4.0-1) ... Setting up libwind0-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up libpython3.8:s390x (3.8.2-1ubuntu1.1) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libevent-dev (2.1.11-stable-1) ... Setting up libgssapi-krb5-2:s390x (1.17-6ubuntu4) ... Setting up libcroco3:s390x (0.6.13-1) ... Setting up libssh-4:s390x (0.9.3-2ubuntu2) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up dwz (0.13-5) ... Setting up libnl-3-dev:s390x (3.4.0-1) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:s390x (2:1.6.9-2ubuntu1) ... Setting up libjs-jquery (3.5.1+dfsg-3) ... Setting up python3-lib2to3 (3.8.2-1ubuntu1) ... Setting up libmaloc-dev (1.5-1) ... Setting up python3-pkg-resources (46.1.3-1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.2-1ubuntu1) ... Setting up dh-python (4.20200315) ... Setting up libibverbs1:s390x (28.0-1ubuntu1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up python3-setuptools (46.1.3-1) ... Setting up ibverbs-providers:s390x (28.0-1ubuntu1) ... Setting up openssh-client (1:8.2p1-4) ... Setting up libhx509-5-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up libxext6:s390x (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxnvctrl0:s390x (440.64-0ubuntu1) ... Setting up libnl-route-3-dev:s390x (3.4.0-1) ... Setting up libltdl-dev:s390x (2.4.6-14) ... Setting up libpython3.8-dev:s390x (3.8.2-1ubuntu1.1) ... Setting up python3.8-dev (3.8.2-1ubuntu1.1) ... Setting up libhwloc-dev:s390x (2.2.0+dfsg-3) ... Setting up libkrb5-26-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up libpython3-dev:s390x (3.8.2-0ubuntu2) ... Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:s390x (28.0-1ubuntu1) ... Setting up libhwloc-plugins:s390x (2.2.0+dfsg-3) ... Setting up libheimntlm0-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up libgssapi3-heimdal:s390x (7.7.0+dfsg-1ubuntu1) ... Setting up python3-dev (3.8.2-0ubuntu2) ... Setting up libpmix2:s390x (3.1.5-1) ... Setting up libopenmpi3:s390x (4.0.3-6ubuntu1) ... Setting up libldap-2.4-2:s390x (2.4.49+dfsg-2ubuntu2) ... Setting up libcurl4:s390x (7.68.0-1ubuntu2) ... Setting up openmpi-bin (4.0.3-6ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up cmake (3.16.3-2ubuntu1) ... Setting up libopenmpi-dev:s390x (4.0.3-6ubuntu1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/openmpi/include to provide /usr/include/s390x-linux-gnu/mpi (mpi-s390x-linux-gnu) in auto mode Setting up mpi-default-dev (1.13) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13ubuntu1) ... Setting up sbuild-build-depends-apbs-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-178-generic s390x (s390x) Toolchain package versions: binutils_2.34-6ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-12ubuntu1 gcc-8_8.4.0-3ubuntu2 gcc-9_9.3.0-12ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-12ubuntu1 libstdc++6_10.1.0-1ubuntu1 linux-libc-dev_5.4.0-29.33 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.0 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-6ubuntu1 binutils-common_2.34-6ubuntu1 binutils-s390x-linux-gnu_2.34-6ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu9 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 cmake_3.16.3-2ubuntu1 cmake-data_3.16.3-2ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-8_8.4.0-3ubuntu2 cpp-9_9.3.0-12ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu9 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-12ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-1ubuntu1 gcc-8_8.4.0-3ubuntu2 gcc-8-base_8.4.0-3ubuntu2 gcc-9_9.3.0-12ubuntu1 gcc-9-base_9.3.0-12ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gfortran-8_8.4.0-3ubuntu2 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-0ubuntu4 hostname_3.23 ibverbs-providers_28.0-1ubuntu1 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 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libnghttp2-14_1.40.0-1build1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.0.3-6ubuntu1 libopenmpi3_4.0.3-6ubuntu1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpciaccess0_0.16-0ubuntu1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2build1 libpmix2_3.1.5-1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-4ubuntu1 libpsl5_0.21.0-1ubuntu1 libpython3-dev_3.8.2-0ubuntu2 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8_3.8.2-1ubuntu1.1 libpython3.8-dev_3.8.2-1ubuntu1.1 libpython3.8-minimal_3.8.2-1ubuntu1.1 libpython3.8-stdlib_3.8.2-1ubuntu1.1 libreadline8_8.0-4 librhash0_1.3.9-1 libroken18-heimdal_7.7.0+dfsg-1ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu1 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu9 libsqlite3-0_3.31.1-5 libss2_1.45.6-1ubuntu1 libssh-4_0.9.3-2ubuntu2 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-12ubuntu1 libstdc++6_10.1.0-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.5-2ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-1ubuntu1 libuchardet0_0.0.6-3build1 libudev1_245.5-2ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu9 libuv1_1.35.0-2ubuntu1 libwind0-heimdal_7.7.0+dfsg-1ubuntu1 libx11-6_2:1.6.9-2ubuntu1 libx11-data_2:1.6.9-2ubuntu1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.14-2 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxml2_2.9.10+dfsg-5 libxnvctrl0_440.64-0ubuntu1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-29.33 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu5 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu9 mpi-default-dev_1.13 ncurses-base_6.2-1 ncurses-bin_6.2-1 node-jquery_3.5.1+dfsg-3 ocl-icd-libopencl1_2.2.11-1ubuntu1 openmpi-bin_4.0.3-6ubuntu1 openmpi-common_4.0.3-6ubuntu1 openssh-client_1:8.2p1-4 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu5 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-4ubuntu1 python3_3.8.2-0ubuntu2 python3-dev_3.8.2-0ubuntu2 python3-distutils_3.8.2-1ubuntu1 python3-lib2to3_3.8.2-1ubuntu1 python3-minimal_3.8.2-0ubuntu2 python3-pkg-resources_46.1.3-1 python3-setuptools_46.1.3-1 python3.8_3.8.2-1ubuntu1.1 python3.8-dev_3.8.2-1ubuntu1.1 python3.8-minimal_3.8.2-1ubuntu1.1 readline-common_8.0-4 sbuild-build-depends-apbs-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 swig_4.0.1-5build1 swig4.0_4.0.1-5build1 systemd_245.5-2ubuntu1 systemd-sysv_245.5-2ubuntu1 systemd-timesyncd_245.5-2ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 util-linux_2.34-0.1ubuntu9 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Apr 3 04:56:54 2020 UTC gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./apbs_1.5+dfsg1-3.dsc dpkg-source: info: extracting apbs in apbs-1.5+dfsg1 dpkg-source: info: unpacking apbs_1.5+dfsg1.orig.tar.xz dpkg-source: info: unpacking apbs_1.5+dfsg1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying debian_make.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying link_libapbs_routines.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19276035 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19276035 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19276035 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 1.5+dfsg1-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/apbs-1.5+dfsg1' dh_auto_clean --sourcedir=apbs make[1]: Leaving directory '/<>/apbs-1.5+dfsg1' dh_clean debian/rules build-arch dh build-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/apbs-1.5+dfsg1' dh_auto_configure --sourcedir=apbs -- \ -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=On \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETK_PATH=/usr -DENABLE_FETK=Off cd obj-s390x-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_AUTOGEN_VERBOSE=ON -DCMAKE_INSTALL_LIBDIR=lib/s390x-linux-gnu -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=On -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETK_PATH=/usr -DENABLE_FETK=Off ../apbs -- The C compiler identification is GNU 9.3.0 -- The CXX compiler identification is GNU 9.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Checking for MPI -- Found MPI_C: /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies m;stdc++;maloc;/usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies m;stdc++;maloc;/usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies m;stdc++;maloc;/usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies m;stdc++;maloc;/usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_routines -- *************************** -- -- APBS Libraries: m;stdc++;maloc;/usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines -- *************************** -- -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Found SWIG: /usr/bin/swig4.0 (found version "4.0.1") -- Found PythonLibs: /usr/lib/s390x-linux-gnu/libpython3.8.so (found version "3.8.2") CMake Deprecation Warning at /usr/share/cmake-3.16/Modules/UseSWIG.cmake:566 (message): SWIG_ADD_MODULE is deprecated. Use SWIG_ADD_LIBRARY instead. Call Stack (most recent call first): tools/python/CMakeLists.txt:11 (SWIG_ADD_MODULE) CMake Warning (dev) at /usr/share/cmake-3.16/Modules/UseSWIG.cmake:607 (message): Policy CMP0078 is not set: UseSWIG generates standard target names. Run "cmake --help-policy CMP0078" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/share/cmake-3.16/Modules/UseSWIG.cmake:567 (swig_add_library) tools/python/CMakeLists.txt:11 (SWIG_ADD_MODULE) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /usr/share/cmake-3.16/Modules/UseSWIG.cmake:460 (message): Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module flag. Run "cmake --help-policy CMP0086" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/share/cmake-3.16/Modules/UseSWIG.cmake:702 (SWIG_ADD_SOURCE_TO_MODULE) /usr/share/cmake-3.16/Modules/UseSWIG.cmake:567 (swig_add_library) tools/python/CMakeLists.txt:11 (SWIG_ADD_MODULE) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_AUTOGEN_VERBOSE CMAKE_EXPORT_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB FETK_PATH -- Build files have been written to: /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu make[1]: Leaving directory '/<>/apbs-1.5+dfsg1' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/apbs-1.5+dfsg1' dh_auto_build --sourcedir=apbs cd obj-s390x-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' /usr/bin/cmake -S/<>/apbs-1.5+dfsg1/apbs -B/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/CMakeFiles /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src/generic /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src/pmgc /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake --color= Scanning dependencies of target apbslib_swig_compilation make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build Scanning dependencies of target apbs_generic make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' Scanning dependencies of target apbs_pmgc make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 1%] Swig compile apbslib.i for python cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/_apbslib.dir [ 2%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 3%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/mgparm.c cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/nosh.c cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python && /usr/bin/cmake -E touch /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp [ 4%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/buildAd.c cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig4.0 -python -outdir /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python -interface _apbslib -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -I/usr/include/python3.8 -I/<>/apbs-1.5+dfsg1/apbs/tools/python -o /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /<>/apbs-1.5+dfsg1/apbs/tools/python/apbslib.i [ 5%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/buildBd.c [ 6%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/buildGd.c [ 8%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/femparm.c make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 8%] Built target apbslib_swig_compilation [ 9%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/buildPd.c [ 10%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/pbamparm.c [ 11%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/pbsamparm.c [ 12%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/pbeparm.c [ 13%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/bemparm.c [ 15%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/cgd.c [ 16%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/gsd.c [ 17%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/matvecd.c [ 18%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/geoflowparm.c [ 19%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/apolparm.c [ 20%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/mgcsd.c [ 22%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vacc.c [ 23%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/mgdrvd.c [ 24%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/valist.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/valist.c [ 25%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/mgsubd.c [ 26%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vatom.c [ 27%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vpbe.c [ 29%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vcap.c [ 30%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/mikpckd.c [ 31%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vclist.c [ 32%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vstring.c [ 33%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vparam.c [ 34%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/generic/vgreen.c [ 36%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/mlinpckd.c [ 37%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/mypdec.c [ 38%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/newtond.c [ 39%] Linking C shared library ../../lib/libapbs_generic.so cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.1 -o ../../lib/libapbs_generic.so.1 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic && /usr/bin/cmake -E cmake_symlink_library ../../lib/libapbs_generic.so.1 ../../lib/libapbs_generic.so.1 ../../lib/libapbs_generic.so make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 39%] Built target apbs_generic [ 40%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/newdrvd.c [ 41%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/powerd.c [ 43%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/smoothd.c [ 44%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/pmgc/mgfasd.c [ 45%] Linking C shared library ../../lib/libapbs_pmgc.so cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.1 -o ../../lib/libapbs_pmgc.so.1 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_symlink_library ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_pmgc.so make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 45%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src/mg /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake --color= Scanning dependencies of target apbs_mg make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 46%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 47%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o [ 48%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/mg/vmgrid.c cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/mg/vgrid.c cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/mg/vpmg.c [ 50%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/mg/vopot.c /<>/apbs-1.5+dfsg1/apbs/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /<>/apbs-1.5+dfsg1/apbs/src/mg/vgrid.c:853:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/mg/vpmgp.c [ 52%] Linking C shared library ../../lib/libapbs_mg.so cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.1 -o ../../lib/libapbs_mg.so.1 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../lib/libapbs_generic.so.1 ../../lib/libapbs_pmgc.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library ../../lib/libapbs_mg.so.1 ../../lib/libapbs_mg.so.1 ../../lib/libapbs_mg.so make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 52%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake --color= Scanning dependencies of target tensor2dx Scanning dependencies of target uhbd_asc2bin Scanning dependencies of target mgmesh make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build Scanning dependencies of target apbs_routines make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 53%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o [ 54%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o [ 55%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/mgmesh.c cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_routines.dir/routines.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/routines.c [ 56%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c: In function ‘main’: /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:97:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:98:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:137:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:138:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:139:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:140:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:155:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:156:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:157:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/tensor2dx.c:158:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Linking C executable ../bin/mgmesh cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 59%] Linking C executable ../bin/uhbd_asc2bin cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 60%] Linking C executable ../bin/tensor2dx cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 60%] Built target mgmesh make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake --color= Scanning dependencies of target mergedx make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 61%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/mergedx.dir/mergedx.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/mergedx.c make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 61%] Built target uhbd_asc2bin make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' Scanning dependencies of target mergedx2 [ 61%] Built target tensor2dx make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 62%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/mergedx2.dir/mergedx2.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/mergedx2.c Scanning dependencies of target analysis make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 63%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/analysis.dir/analysis.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/analysis.c [ 65%] Linking C executable ../bin/analysis cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysis.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/analysis.dir/analysis.c.o -o ../bin/analysis ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 66%] Linking C executable ../bin/mergedx cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 66%] Built target analysis make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake --color= Scanning dependencies of target del2dx make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 68%] Linking C executable ../bin/mergedx2 [ 68%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/del2dx.dir/del2dx.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/del2dx.c /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 68%] Built target mergedx make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake --color= /<>/apbs-1.5+dfsg1/apbs/src/routines.c: In function ‘writematMG’: /<>/apbs-1.5+dfsg1/apbs/src/routines.c:1808:30: warning: ‘-PE’ directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1808 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem, rank); | ^~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1038 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:1832:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1832 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/del2dx.c: In function ‘main’: /<>/apbs-1.5+dfsg1/apbs/tools/mesh/del2dx.c:76:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/del2dx.c:89:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/del2dx.c:97:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/del2dx.c:103:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/tools/mesh/del2dx.c:106:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scanning dependencies of target dxmath make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 69%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/dxmath.dir/dxmath.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/dxmath.c make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 69%] Built target mergedx2 make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake --color= Scanning dependencies of target benchmark make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 70%] Linking C executable ../bin/del2dx cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 [ 72%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/benchmark.dir/benchmark.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/benchmark.c make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 72%] Built target del2dx make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/value.dir/DependInfo.cmake --color= [ 73%] Linking C executable ../bin/benchmark cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 Scanning dependencies of target value make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/benchmark.dir/benchmark.c.o -o ../bin/benchmark ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 74%] Linking C executable ../bin/dxmath cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 [ 75%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/value.dir/value.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/value.c /<>/apbs-1.5+dfsg1/apbs/src/routines.c: In function ‘writedataMG’: /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2668:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2668 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2712:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2712 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2703:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2703 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2686:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2686 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2679:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2679 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2693:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2693 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/dxmath.dir/dxmath.c.o -o ../bin/dxmath ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2658:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2658 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 75%] Built target benchmark make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/similarity.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 76%] Linking C executable ../bin/value cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 [ 76%] Built target dxmath make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend Scanning dependencies of target similarity make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/value.dir/value.c.o -o ../bin/value ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 77%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/similarity.dir/similarity.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/similarity.c Scanning dependencies of target dx2mol make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 79%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/dx2mol.c make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 79%] Built target value make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake --color= Scanning dependencies of target smooth make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 80%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/smooth.dir/smooth.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/smooth.c [ 81%] Linking C executable ../bin/dx2mol cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 81%] Built target dx2mol make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake --color= Scanning dependencies of target multivalue make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 82%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/multivalue.dir/multivalue.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/multivalue.c [ 83%] Linking C executable ../bin/similarity cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/similarity.dir/similarity.c.o -o ../bin/similarity ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 84%] Linking C executable ../bin/smooth cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 84%] Built target similarity make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/dx2uhbd.dir/DependInfo.cmake --color= [ 86%] Linking C executable ../bin/multivalue make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 [ 86%] Built target smooth /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/multivalue.dir/multivalue.c.o -o ../bin/multivalue ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake --color= Scanning dependencies of target dx2uhbd make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 87%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/mesh/dx2uhbd.c Scanning dependencies of target born make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 88%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/born.dir/born.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/manip/born.c make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 88%] Built target multivalue make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake --color= [ 89%] Linking C executable ../bin/dx2uhbd cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 Scanning dependencies of target coulomb make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 90%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/coulomb.dir/coulomb.c.o -c /<>/apbs-1.5+dfsg1/apbs/tools/manip/coulomb.c [ 91%] Linking C executable ../bin/born cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/born.dir/born.c.o -o ../bin/born ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 91%] Built target dx2uhbd [ 93%] Linking C shared library ../lib/libapbs_routines.so cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.1 -o ../lib/libapbs_routines.so.1 CMakeFiles/apbs_routines.dir/routines.c.o -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../lib/libapbs_mg.so.1 ../lib/libapbs_generic.so.1 ../lib/libapbs_pmgc.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 94%] Linking C executable ../bin/coulomb cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../lib/libapbs_mg.so.1 ../../lib/libapbs_pmgc.so.1 ../../lib/libapbs_generic.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library ../lib/libapbs_routines.so.1 ../lib/libapbs_routines.so.1 ../lib/libapbs_routines.so [ 94%] Built target born make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 94%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake --color= Scanning dependencies of target apbs make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' Scanning dependencies of target _apbslib make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 95%] Building C object src/CMakeFiles/apbs.dir/main.c.o [ 96%] Building C object src/CMakeFiles/apbs.dir/routines.c.o cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/apbs.dir/main.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/main.c make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src && /usr/bin/cc -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fopenmp -o CMakeFiles/apbs.dir/routines.c.o -c /<>/apbs-1.5+dfsg1/apbs/src/routines.c [ 97%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o [ 97%] Built target coulomb cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/usr/lib/s390x-linux-gnu/openmpi/include -I/<>/apbs-1.5+dfsg1/apbs/src -I/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src -I/<>/apbs-1.5+dfsg1/apbs/include -I/usr/include/python3.8 -I/<>/apbs-1.5+dfsg1/apbs/tools/python -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fopenmp -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /<>/apbs-1.5+dfsg1/apbs/src/main.c: In function ‘main’: /<>/apbs-1.5+dfsg1/apbs/src/main.c:288:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 288 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/main.c:288:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 288 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c: In function ‘writematMG’: /<>/apbs-1.5+dfsg1/apbs/src/routines.c:1808:30: warning: ‘-PE’ directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1808 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem, rank); | ^~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1038 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:1832:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1832 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c: In function ‘writedataMG’: /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2668:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2668 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2712:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2712 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2703:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2703 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2686:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2686 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2679:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2679 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2693:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2693 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs-1.5+dfsg1/apbs/src/routines.c:2658:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2658 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs-1.5+dfsg1/apbs/src/apbs.h:67, from /<>/apbs-1.5+dfsg1/apbs/src/routines.h:64, from /<>/apbs-1.5+dfsg1/apbs/src/routines.c:54: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Linking C executable ../bin/apbs cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/apbs.dir/main.c.o CMakeFiles/apbs.dir/routines.c.o -o ../bin/apbs -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../lib/libapbs_routines.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../lib/libapbs_mg.so.1 ../lib/libapbs_generic.so.1 ../lib/libapbs_pmgc.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 98%] Built target apbs [100%] Linking C shared module ../../lib/_apbslib.so cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>/apbs-1.5+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o ../../lib/_apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../lib/libapbs_routines.so.1 /usr/lib/s390x-linux-gnu/libpython3.8.so ../../lib/libapbs_mg.so.1 ../../lib/libapbs_generic.so.1 ../../lib/libapbs_pmgc.so.1 -lm -lstdc++ -lmaloc /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python && /usr/bin/cmake -E copy /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/apbslib.py /<>/apbs-1.5+dfsg1/apbs/../pdb2pqr/pdb2pka cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python && /usr/bin/cmake -E copy /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/lib/_apbslib.so /<>/apbs-1.5+dfsg1/apbs/../pdb2pqr/pdb2pka make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [100%] Built target _apbslib make[3]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[1]: Leaving directory '/<>/apbs-1.5+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/apbs-1.5+dfsg1' (cd apbs/tests; PATH=/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/bin:${PATH} LD_LIBRARY_PATH=/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/lib:${LD_LIBRARY_PATH} python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) 1.5 ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-auto.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-auto.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605695E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 61.272 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.272 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.199 MB total, 122.094 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.094 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-auto.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.313 MB total, 1028.313 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.313 MB total, 2042.104 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.282 MB total, 2042.104 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.282 MB total, 2046.039 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.437 MB total, 2046.039 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.437 MB total, 2069.483 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058621E+02 kJ/mol Global net ELEC energy = 1.048683058621E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.483 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-auto.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.313 MB total, 1028.313 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.313 MB total, 2042.104 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.282 MB total, 2042.104 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.282 MB total, 2046.039 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.437 MB total, 2046.039 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.437 MB total, 2069.483 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077688E+02 kJ/mol Global net ELEC energy = 1.095841077688E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.483 MB high water Thanks for using APBS! Testing all sections The following sections will be tested: born, actin-dimer-auto, actin-dimer-parallel, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv, protein-rna ================================================================================ Running tests for born section -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.in Checking Polar Forces Checking Apolar Forces Elapsed time: 0.000916 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermidiate energies in input file apbs-mol-auto.out Testing computed result 9.607073836227E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 2.200266567971E+03 against expected result 2.200267E+03 *** PASSED *** Testing computed result 4.732245131587E+03 against expected result 4.732245E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.297735526282E+02 against expected result -2.297735E+02 *** PASSED *** Elapsed time: 1.011970 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermidiate energies in input file apbs-smol-auto.out Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 2.201243880085E+03 against expected result 2.201244E+03 *** PASSED *** Testing computed result 4.733006258977E+03 against expected result 4.733006E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.290124252387E+02 against expected result -2.290124E+02 *** PASSED *** Elapsed time: 1.157030 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 2.401768459022E+02 8.142935592471E+02 1.485255308186E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.761864094552E+01 Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 2.401768459022E+02 8.142778312125E+02 1.485246667424E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.762728170718E+01 Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 2.401768459091E+02 8.142935605695E+02 1.485255306569E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.761864257239E+01 Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 2.401768459091E+02 8.142778325440E+02 1.485246665692E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.762728344953E+01 Testing computed result 9.607073836226E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 3.257142783573E+03 against expected result 3.257143E+03 *** PASSED *** Testing computed result 5.941003947871E+03 against expected result 5.941004E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.304918486746E+02 against expected result -2.304918E+02 *** PASSED *** Elapsed time: 5.822102 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 2.383232191816E+02 8.145369591602E+02 1.485524998001E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734895113069E+01 Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 2.383232191816E+02 8.145419898332E+02 1.485529328612E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734462051928E+01 Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 2.383232191909E+02 8.145369593489E+02 1.485524997676E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734895146550E+01 Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 2.383232191909E+02 8.145419900310E+02 1.485529328301E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734462084052E+01 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 3.258157898373E+03 against expected result 3.258158E+03 *** PASSED *** Testing computed result 5.942108652590E+03 against expected result 5.942109E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.293871439560E+02 against expected result -2.293871E+02 *** PASSED *** Elapsed time: 5.258420 seconds -------------------------------------------------------------------------------- Total elapsed time: 13.250438 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-auto section -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermidiate energies in input file apbs-mol-auto.out Testing computed result 1.527617850342E+05 against expected result 1.527618E+05 *** PASSED *** Testing computed result 2.919510754196E+05 against expected result 2.919511E+05 *** PASSED *** Testing computed result 1.527671844880E+05 against expected result 1.527672E+05 *** PASSED *** Testing computed result 2.915468859278E+05 against expected result 2.915469E+05 *** PASSED *** Testing computed result 3.056317807611E+05 against expected result 3.056318E+05 *** PASSED *** Testing computed result 5.836028296532E+05 against expected result 5.836028E+05 *** PASSED *** Testing computed result 1.048683058621E+02 against expected result 1.048683E+02 *** PASSED *** Elapsed time: 75.004337 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermidiate energies in input file apbs-smol-auto.out Testing computed result 1.528632421825E+05 against expected result 1.528632E+05 *** PASSED *** Testing computed result 2.920618662320E+05 against expected result 2.920619E+05 *** PASSED *** Testing computed result 1.529297900572E+05 against expected result 1.529298E+05 *** PASSED *** Testing computed result 2.916592202835E+05 against expected result 2.916592E+05 *** PASSED *** Testing computed result 3.059244262535E+05 against expected result 3.059244E+05asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.335181353180E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.307364296734E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.892640552270E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.287358143371E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.237489755360E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595556932858E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.344927525614E+00 kJ/mol Global net ELEC energy = 8.344927525614E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161150884899E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.271350510933E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.084559511557E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.159029781186E-02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161009682231E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.271251267660E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -9.008424333884E-01 kJ/mol Global net ELEC energy = -9.008424333884E-01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.533327920982E+01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.349327483109E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.753646268927E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.716901575464E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.760706267384E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.753396861378E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.002011083294E+01 kJ/mol Global net ELEC energy = 3.002011083294E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.803290534287E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.400275505449E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.150603559111E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.573366340513E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.804039178218E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.400354034488E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.710240552064E+00 kJ/mol Global net ELEC energy = 8.710240552064E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE4.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.015087619451E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.216054444942E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.620207421716E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.273875108812E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.666622027749E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306246500367E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.108471049009E+01 kJ/mol Global net ELEC energy = 2.108471049009E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE5.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.100112513614E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.662571945373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.370921758038E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.012777153962E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.115105077953E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.662769018146E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.372005444809E+00 kJ/mol Global net ELEC energy = 2.372005444809E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE6.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.817378781616E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.959534462269E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176793266728E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.643533578081E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176229449467E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.643148330287E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.892943480303E+00 kJ/mol Global net ELEC energy = -1.892943480303E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-parallel-PE7.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.428230292158E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.199832997920E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.881300088062E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.152799174875E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.847712854852E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618156668929E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.043753521021E+01 kJ/mol Global net ELEC energy = 3.043753521021E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.371266245949E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.306912290219E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977036667733E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.288057507497E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.356039288708E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595843060209E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.732624922090E+00 kJ/mol Global net ELEC energy = 8.732624922090E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183935033618E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.276169789420E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.420924995464E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.129030298944E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183791435221E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.276043001853E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.154972633314E+00 kJ/mol Global net ELEC energy = -1.154972633314E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.992726432058E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.375960934473E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.863608503641E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.720602537782E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.896854387650E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.757590620855E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.228473728522E+01 kJ/mol Global net ELEC energy = 3.228473728522E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.826846317904E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.401007397614E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.966525690477E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.961424692860E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827933209233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.401092487740E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 9.405155088186E+00 kJ/mol Global net ELEC energy = 9.405155088186E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE4.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.021998204986E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.215581391535E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.644646339930E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.274227987774E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.689865332202E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306747563963E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.637622734662E+01 kJ/mol Global net ELEC energy = 3.637622734662E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE5.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.187673595319E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.663590090053E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.710032885061E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.848912615891E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189033693728E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.663642086377E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 1.004854500183E+00 kJ/mol Global net ELEC energy = 1.004854500183E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE6.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.897659240526E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.552765434658E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.200266111088E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.646358551314E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.199560371894E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.645933328248E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.699465221137E+00 kJ/mol Global net ELEC energy = -1.699465221137E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-parallel-PE7.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 274.665 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.521894873214E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.665 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200161660501E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 534.807 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.033680106430E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.633 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.154432431334E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 538.742 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.960165191413E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.788 MB total, 562.186 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618664307349E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.059403714563E+01 kJ/mol Global net ELEC energy = 3.059403714563E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.186 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file alkanes.in... rank 0 size 1... read Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.246 MB high water Thanks for using APBS! *** PASSED *** Testing computed result 5.838306706232E+05 against expected result 5.838307E+05 *** PASSED *** Testing computed result 1.095841077688E+02 against expected result 1.095841E+02 *** PASSED *** Elapsed time: 57.420607 seconds -------------------------------------------------------------------------------- Total elapsed time: 132.424944 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-parallel section -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 8 separate files using the inputgen utility Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 1.335181353180E+03 1.307364296734E+04 2.892640552270E+03 2.287358143371E+04 4.237489755360E+03 3.595556932858E+04 8.344927525614E+00 Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 1.161150884899E+04 9.271350510933E+04 1.084559511557E-01 9.159029781186E-02 1.161009682231E+04 9.271251267660E+04 -9.008424333884E-01 Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 1.533327920982E+01 3.349327483109E+02 4.753646268927E+03 3.716901575464E+04 4.760706267384E+03 3.753396861378E+04 3.002011083294E+01 Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 1.803290534287E+04 1.400275505449E+05 8.150603559111E-01 8.573366340513E-01 1.804039178218E+04 1.400354034488E+05 8.710240552064E+00 Checking for intermidiate energies in input file apbs-mol-parallel-PE4.out Processor 4 results: 4.015087619451E+02 3.216054444942E+03 1.620207421716E+04 1.273875108812E+05 1.666622027749E+04 1.306246500367E+05 2.108471049009E+01 Checking for intermidiate energies in input file apbs-mol-parallel-PE5.out Processor 5 results: 2.100112513614E+03 1.662571945373E+04 4.370921758038E-01 4.012777153962E-01 2.115105077953E+03 1.662769018146E+04 2.372005444809E+00 Checking for intermidiate energies in input file apbs-mol-parallel-PE6.out Processor 6 results: 2.817378781616E+00 1.959534462269E+00 1.176793266728E+04 9.643533578081E+04 1.176229449467E+04 9.643148330287E+04 -1.892943480303E+00 Checking for intermidiate energies in input file apbs-mol-parallel-PE7.out Processor 7 results: 2.428230292158E+03 2.199832997920E+04 3.881300088062E+02 4.152799174875E+03 2.847712854852E+03 2.618156668929E+04 3.043753521021E+01 Testing computed result 3.592759777075E+04 against expected result 3.592760E+04 *** PASSED *** Testing computed result 2.879916947822E+05 against expected result 2.879917E+05 *** PASSED *** Testing computed result 3.600578432293E+04 against expected result 3.600578E+04 *** PASSED *** Testing computed result 2.880195932299E+05 against expected result 2.880196E+05 *** PASSED *** Testing computed result 7.204001733220E+04 against expected result 7.204002E+04 *** PASSED *** Testing computed result 5.761028442781E+05 against expected result 5.761028E+05 *** PASSED *** Testing computed result 9.817574414204E+01 against expected result 9.817456E+01 *** PASSED (with rounding error - see log) *** Elapsed time: 205.841766 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 8 separate files using the inputgen utility Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 1.371266245949E+03 1.306912290219E+04 2.977036667733E+03 2.288057507497E+04 4.356039288708E+03 3.595843060209E+04 8.732624922090E+00 Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 1.183935033618E+04 9.276169789420E+04 1.420924995464E-01 1.129030298944E-01 1.183791435221E+04 9.276043001853E+04 -1.154972633314E+00 Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 9.992726432058E+00 3.375960934473E+02 4.863608503641E+03 3.720602537782E+04 4.896854387650E+03 3.757590620855E+04 3.228473728522E+01 Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 1.826846317904E+04 1.401007397614E+05 9.966525690477E-01 8.961424692860E-01 1.827933209233E+04 1.401092487740E+05 9.405155088186E+00 Checking for intermidiate energies in input file apbs-smol-parallel-PE4.out Processor 4 results: 4.021998204986E+02 3.215581391535E+03 1.644646339930E+04 1.274227987774E+05 1.689865332202E+04 1.306747563963E+05 3.637622734662E+01 Checking for intermidiate energies in input file apbs-smol-parallel-PE5.out Processor 5 results: 2.187673595319E+03 1.663590090053E+04 4.710032885061E-01 4.848912615891E-01 2.189033693728E+03 1.663642086377E+04 1.004854500183E+00 Checking for intermidiate energies in input file apbs-smol-parallel-PE6.out Processor 6 results: 4.897659240526E+00 2.552765434658E+00 1.200266111088E+04 9.646358551314E+04 1.199560371894E+04 9.645933328248E+04 -1.699465221137E+00 Checking for intermidiate energies in input file apbs-smol-parallel-PE7.out Processor 7 results: 2.521894873214E+03 2.200161660501E+04 4.033680106430E+02 4.154432431334E+03 2.960165191413E+03 2.618664307349E+04 3.059403714563E+01 Testing computed result 3.660573843587E+04 against expected result 3.660574E+04 *** PASSED *** Testing computed result 2.881248083137E+05 against expected result 2.881248E+05 *** PASSED *** Testing computed result 3.669474744055E+04 against expected result 3.669475E+04 *** PASSED *** Testing computed result 2.881289111114E+05 against expected result 2.881289E+05 *** PASSED *** Testing computed result 7.341359604700E+04 against expected result 7.341360E+04 *** PASSED *** Testing computed result 5.763611692192E+05 against expected result 5.763611E+05 *** PASSED *** Testing computed result 1.155431984335E+02 against expected result 1.155421E+02 *** PASSED (with rounding error - see log) *** Elapsed time: 184.129421 seconds -------------------------------------------------------------------------------- Total elapsed time: 389.971187 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for alkanes section -------------------------------------------------------------------------------- Testing input file alkanes.in Checking for intermidiate energies in input file alkanes.out Testing computed result 1.439739455792E+01 against expected result 1.439739E+01 *** PASSED *** Testing computed result 1.208346456826E+01 against expected result 1.208346E+01 *** PASSED *** Testing computed result 1.354016672221E+01 against expected result 1.354017E+01 *** PASSED *** Testing computed result 9.363673200142E+00 against expected result 9.363673E+00 *** PASSED *** Testing computed result 9.422717598546E+00 against expected result 9.422718E+00 *** PASSED *** Testing computed result 1.640068943201E+01 against expected result 1.640069E+01 *** PASSED *** Testing computed result 1.323144287435E+01 against expected result 1.323144E+01 *** PASSED *** Testing computed result 7.894367190329E+00 against expected result 7.894367E+00 *** PASSED *** Testing computed result 1.449633815052E+01 against expected result 1.449634E+01 *** PASSED *** Testing computed result 1.447900211546E+01 against expected result 1.447900E+01 *** PASSED *** Testing computed result 1.192358496286E+01 against expected result 1.192358E+01 *** PASSED *** Elapsed time: 16.334116 seconds -------------------------------------------------------------------------------- Total elapsed time: 16.334116 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for FKBP section --------------------------------------------------------------------------------asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.036 MB total, 122.036 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.036 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.036 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.036 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086373E+01 kJ/mol Global net ELEC energy = 1.500810086373E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.672 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.036 MB total, 122.036 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.036 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.036 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.036 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.404 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.712 MB total, 221.672 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192074E+01 kJ/mol Global net ELEC energy = 1.624454192074E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.672 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.401 MB total, 122.401 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.401 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.401 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.401 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933664E+01 kJ/mol Global net ELEC energy = 1.442499933664E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.281 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.401 MB total, 122.401 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.401 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.401 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.401 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.504 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.953 MB total, 222.281 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742843E+01 kJ/mol Global net ELEC energy = 1.545150742843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.281 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.715 MB total, 62.715 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.715 MB total, 123.689 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.715 MB total, 123.689 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.504 MB total, 146.504 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.504 MB total, 245.081 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.504 MB total, 245.081 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.914 MB total, 245.081 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.914 MB total, 245.714 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.914 MB total, 245.714 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812684E+01 kJ/mol Global net ELEC energy = -5.246475812684E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.714 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.715 MB total, 62.715 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.715 MB total, 123.689 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.715 MB total, 123.689 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.504 MB total, 146.504 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.504 MB total, 245.081 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.504 MB total, 245.081 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.914 MB total, 245.081 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.914 MB total, 245.714 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.914 MB total, 245.714 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017059E+01 kJ/mol Global net ELEC energy = -5.405979017059E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.714 MB high water Thanks for using APBS! Testing input file 1d7h-dmso-mol.in Checking for intermidiate energies in input file 1d7h-dmso-mol.out Testing computed result 1.060899690259E+04 against expected result 1.060900E+04 *** PASSED *** Testing computed result 4.276523673491E+04 against expected result 4.276524E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.961107503213E+01 against expected result 3.961108E+01 *** PASSED *** Testing computed result 7.121048606059E+02 against expected result 7.121049E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.058410584089E+04 against expected result 1.058411E+04 *** PASSED *** Testing computed result 4.205385249581E+04 against expected result 4.205385E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.500810086373E+01 against expected result 1.500810E+01 *** PASSED *** Elapsed time: 8.686895 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in Checking for intermidiate energies in input file 1d7h-dmso-smol.out Testing computed result 1.074948704824E+04 against expected result 1.074949E+04 *** PASSED *** Testing computed result 4.289487256481E+04 against expected result 4.289487E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.719709905887E+01 against expected result 3.719710E+01 *** PASSED *** Testing computed result 7.125747080979E+02 against expected result 7.125747E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.071654753674E+04 against expected result 1.071655E+04 *** PASSED *** Testing computed result 4.218178203716E+04 against expected result 4.218178E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.624454192074E+01 against expected result 1.624454E+01 *** PASSED *** Elapsed time: 8.545086 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in Checking for intermidiate energies in input file 1d7i-dss-mol.out Testing computed result 9.160578033846E+03 against expected result 9.160578E+03 *** PASSED *** Testing computed result 3.955701871716E+04 against expected result 3.955702E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 9.431133325426E+01 against expected result 9.431133E+01 *** PASSED *** Testing computed result 1.677348113184E+03 against expected result 1.677348E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.040108332204E+03 against expected result 9.040108E+03 *** PASSED *** Testing computed result 3.787747796627E+04 against expected result 3.787748E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.442499933664E+01 against expected result 1.442501E+01 *** PASSED *** Elapsed time: 8.617274 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in Checking for intermidiate energies in input file 1d7i-dss-smol.out Testing computed result 9.634884642408E+03 against expected result 9.634885E+03 *** PASSED *** Testing computed result 4.003177540425E+04 against expected result 4.003178E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 7.942232645345E+01 against expected result 7.942233E+01 *** PASSED *** Testing computed result 1.677798535473E+03 against expected result 1.677799E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.507068451372E+03 against expected result 9.507068E+03 *** PASSED *** Testing computed result 3.835075772299E+04 against expected result 3.835076E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.545150742843E+01 against expected result 1.545150E+01 *** PASSED *** Elapsed time: 8.606309 seconds -------------------------------------------------------------------------------- Total elapsed time: 34.455564 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for hca-bind section -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermidiate energies in input file apbs-mol.out Testing computed result 2.213600726771E+02 against expected result 2.213601E+02 *** PASSED *** Testing computed result 1.825764811255E+03 against expected result 1.825765E+03 *** PASSED *** Testing computed result 6.458471211905E+03 against expected result 6.458471E+03 *** PASSED *** Testing computed result 2.093606095527E+04 against expected result 2.093606E+04 *** PASSED *** Testing computed result 1.515433544464E+05 against expected result 1.515434E+05 *** PASSED *** Testing computed result 1.786369323561E+05 against expected result 1.786369E+05 *** PASSED *** Testing computed result 2.105322784838E+04 against expected result 2.105323E+04 *** PASSED *** Testing computed result 1.533304996252E+05 against expected result 1.533305E+05 *** PASSED *** Testing computed result 1.850429388099E+05 against expected result 1.850429E+05 *** PASSED *** Testing computed result -5.246475812684E+01 against expected result -5.246476E+01 *** PASSED *** Elapsed time: 8.096822 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermidiate energies in input file apbs-smol.out Testing computed result 1.884888131017E+02 against expected result 1.884888E+02 *** PASSED *** Testing computed result 1.820045922544E+03 against expected result 1.820046E+03 *** PASSED *** Testing computed result 6.460002606908E+03 against expected result 6.460003E+03 *** PASSED *** Testing computed result 2.189161497021E+04 against expected result 2.189161E+04 *** PASSED *** Testing computed result 1.520000494925E+05 against expected result 1.520000E+05 *** PASSED *** Testing computed result 1.790436191580E+05 against expected result 1.790436E+05 ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 61.581 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.394 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.394 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.355 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.355 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.386 MB high water Thanks for using APBS! ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 61.581 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.404 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.394 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.394 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.355 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.355 MB total, 122.386 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.386 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file ion-pmf.in... rank 0 size 1... read Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.100 MB total, 61.100 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.100 MB total, 61.149 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.128e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.766e-05 tot 1 -2.723e-02 9.131e-07 9.134e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.768e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718345777E+00 WCA energy for atom 1: -6.909411348230E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365306965532E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365306965532E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.244 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-vdw.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.280 MB total, 204.280 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.280 MB total, 405.989 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.139 MB total, 405.989 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.139 MB total, 533.414 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.052 MB total, 533.414 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.052 MB total, 534.794 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648803E+00 kJ/mol Global net ELEC energy = 8.083515648803E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.794 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-vdw.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.280 MB total, 204.280 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.280 MB total, 405.989 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.139 MB total, 405.989 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.139 MB total, 533.414 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.052 MB total, 533.414 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.052 MB total, 534.794 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255720E+01 kJ/mol Global net ELEC energy = 2.096300255720E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.794 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol-surf.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.865 MB total, 203.865 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.865 MB total, 405.574 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.509 MB total, 405.574 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.509 MB total, 493.783 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.846 MB total, 493.783 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.846 MB total, 494.589 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686582E+02 kJ/mol Global net ELEC energy = 1.192607686582E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.589 MB high water Thanks for using APBS! *** PASSED *** Testing computed result 2.195842512312E+04 against expected result 2.195843E+04 *** PASSED *** Testing computed result 1.537771604355E+05 against expected result 1.537772E+05 *** PASSED *** Testing computed result 1.854495619747E+05 against expected result 1.854496E+05 *** PASSED *** Testing computed result -5.405979017059E+01 against expected result -5.405978E+01 *** PASSED *** Elapsed time: 8.472851 seconds -------------------------------------------------------------------------------- Total elapsed time: 16.569673 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ionize section -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermidiate energies in input file apbs-mol.out Testing computed result 5.823898055191E+03 against expected result 5.823898E+03 *** PASSED *** Testing computed result 9.793274462353E+03 against expected result 9.793274E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.219846763777E+03 against expected result 8.219847E+03 *** PASSED *** Testing computed result 1.392741988698E+04 against expected result 1.392742E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.862359524598E+03 against expected result 3.862360E+03 *** PASSED *** Testing computed result 6.288156251610E+03 against expected result 6.288156E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.267882018629E+01 against expected result -2.267882E+01 *** PASSED *** Testing computed result -1.997462636633E+02 against expected result -1.997463E+02 *** PASSED *** Testing computed result -2.974598403628E+02 against expected result -2.974598E+02 *** PASSED *** Testing computed result -4.745272838398E+02 against expected result -4.745273E+02 *** PASSED *** Elapsed time: 1.934839 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermidiate energies in input file apbs-smol.out Testing computed result 5.824172730822E+03 against expected result 5.824173E+03 *** PASSED *** Testing computed result 9.793622759239E+03 against expected result 9.793623E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.221328580569E+03 against expected result 8.221329E+03 *** PASSED *** Testing computed result 1.392867783119E+04 against expected result 1.392868E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.863066835285E+03 against expected result 3.863067E+03 *** PASSED *** Testing computed result 6.289649216644E+03 against expected result 6.289649E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.233052329981E+01 against expected result -2.233050E+01 *** PASSED *** Testing computed result -1.984883194538E+02 against expected result -1.984883E+02 *** PASSED *** Testing computed result -2.959668753288E+02 against expected result -2.959669E+02 *** PASSED *** Testing computed result -4.721246714828E+02 against expected result -4.721247E+02 *** PASSED *** Elapsed time: 1.825466 seconds -------------------------------------------------------------------------------- Total elapsed time: 3.760305 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-pmf section -------------------------------------------------------------------------------- Testing input file ion-pmf.in Checking for intermidiate energies in input file ion-pmf.out Testing computed result 7.839535983197E+03 against expected result 7.839536E+03 *** PASSED *** Testing computed result 8.964727588811E+03 against expected result 8.964728E+03 *** PASSED *** Testing computed result -1.125191605614E+03 against expected result -1.125192E+03 *** PASSED *** Elapsed time: 9.301952 seconds -------------------------------------------------------------------------------- Total elapsed time: 9.301952 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for pka-lig section -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in Checking for intermidiate energies in input file apbs-mol-vdw.out Testing computed result 2.224988750664E+03 against expected result 2.224989E+03 *** PASSED *** Testing computed result 1.049695084686E+04 against expected result 1.049695E+04 *** PASSED *** Testing computed result 1.818450789522E+05 against expected result 1.818451E+05 *** PASSED *** Testing computed result 3.008254338259E+05 against expected result 3.008254E+05 *** PASSED *** Testing computed result 1.840918409896E+05 against expected result 1.840918E+05 *** PASSED *** Testing computed result 3.113304681884E+05 against expected result 3.113305E+05 *** PASSED *** Testing computed result 8.083515648803E+00 against expected result 8.083516E+00 *** PASSED *** Elapsed time: 10.224698 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in Checking for intermidiate energies in input file apbs-smol-vdw.out Testing computed result 2.226793167046E+03 against expected result 2.226793E+03 *** PASSED *** Testing computed result 1.050504485887E+04 against expected result 1.050504E+04 *** PASSED *** Testing computed result 1.827976621645E+05 against expected result 1.827977E+05 *** PASSED *** Testing computed result 3.017228546773E+05 against expected result 3.017229E+05 *** PASSED *** Testing computed result 1.850819075387E+05 against expected result 1.850819E+05 *** PASSED *** Testing computed result 3.122488625388E+05 against expected result 3.122489E+05 *** PASSED *** Testing computed result 2.096300255720E+01 against expected result 2.096296E+01 *** PASSED *** Elapsed time: 9.441214 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in Checking for intermidiate energies in input file apbs-mol-surf.out Testing computed result 2.244350164274E+03 against expected result 2.244350E+03 *** PASSED *** Testing computed result 1.052149475373E+04 against expected result 1.052149E+04 *** PASSED *** Testing computed result 1.862615690066E+05 against expected result 1.862616E+05 *** PASSED *** Testing computed result 3.051810884053E+05 against expected result 3.051811E+05 *** PASSED *** Testing computed result 1.886625455219E+05 against expected result 1.886625E+05 *** PASSED *** Testing computed result 3.158218439277E+05 against expected result 3.158218E+05 *** PASSED *** Testing computed result 1.192607686582E+02 against expected result 1.192608E+02 *** PASSED *** Elapsed time: 8.823493 seconds -------------------------------------------------------------------------------- --------------------------------------------------------------------------------asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol-surf.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.865 MB total, 203.865 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.865 MB total, 405.574 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.509 MB total, 405.574 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.509 MB total, 493.783 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.846 MB total, 493.783 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.846 MB total, 494.589 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.589 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file complex-0_1.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.054 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.061 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.062 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.062 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file complex-0_2.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.054 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.061 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.062 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086751E+00 kJ/mol Global net ELEC energy = 8.906694086751E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.062 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file complex-0_3.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.054 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.061 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.062 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.062 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file complex-0_4.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.054 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.054 MB total, 61.061 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.055 MB total, 61.062 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.062 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-mol.in... rank 0 size 1... read Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.245 MB total, 61.245 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.245 MB total, 61.320 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.242 MB total, 61.320 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.242 MB total, 61.320 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.320 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-smol.in... rank 0 size 1... read Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.245 MB total, 61.245 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.245 MB total, 61.320 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.242 MB total, 61.320 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.242 MB total, 61.320 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772492E+01 kJ/mol Global net ELEC energy = -3.757593772492E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.320 MB high water Thanks for using APBS! Testing input file apbs-smol-surf.in Checking for intermidiate energies in input file apbs-smol-surf.out Testing computed result 2.251466789420E+03 against expected result 2.251467E+03 *** PASSED *** Testing computed result 1.052814502873E+04 against expected result 1.052815E+04 *** PASSED *** Testing computed result 1.864071689626E+05 against expected result 1.864072E+05 *** PASSED *** Testing computed result 3.053319953673E+05 against expected result 3.053320E+05 *** PASSED *** Testing computed result 1.888027142979E+05 against expected result 1.888027E+05 *** PASSED *** Testing computed result 3.159690177241E+05 against expected result 3.159690E+05 *** PASSED *** Testing computed result 1.088773280806E+02 against expected result 1.088773E+02 *** PASSED *** Elapsed time: 8.705887 seconds -------------------------------------------------------------------------------- Total elapsed time: 37.195292 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for point-pmf section -------------------------------------------------------------------------------- Testing input file complex-0_1.in Checking for intermidiate energies in input file complex-0_1.out Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 8.975920687031E+01 against expected result 8.975921E+01 *** PASSED *** Testing computed result 2.058277719334E+02 against expected result 2.058278E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 8.975920000000E+01 against expected result 8.975920E+01 *** PASSED *** Testing computed result 2.058280000000E+02 against expected result 2.058280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 8.861510000000E+01 against expected result 8.861510E+01 *** PASSED *** Testing computed result 2.011060000000E+02 against expected result 2.011060E+02 *** PASSED *** Testing computed result 1.830820799027E+01 against expected result 1.830821E+01 *** PASSED *** Elapsed time: 0.393822 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in Checking for intermidiate energies in input file complex-0_2.out Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.084282010393E+02 against expected result 2.084282E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.084280000000E+02 against expected result 2.084280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006560000000E+02 against expected result 1.006560E+02 *** PASSED *** Testing computed result 2.038300000000E+02 against expected result 2.038300E+02 *** PASSED *** Testing computed result 8.906694086751E+00 against expected result 8.906694E+00 *** PASSED *** Elapsed time: 0.362290 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in Checking for intermidiate energies in input file complex-0_3.out Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.337661883222E+02 against expected result 1.337662E+02 *** PASSED *** Testing computed result 2.374361452120E+02 against expected result 2.374361E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.337660000000E+02 against expected result 1.337660E+02 *** PASSED *** Testing computed result 2.374360000000E+02 against expected result 2.374360E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.326720000000E+02 against expected result 1.326720E+02 *** PASSED *** Testing computed result 2.329240000000E+02 against expected result 2.329240E+02 *** PASSED *** Testing computed result 5.909599816984E+00 against expected result 5.909600E+00 *** PASSED *** Elapsed time: 0.365151 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in Checking for intermidiate energies in input file complex-0_4.out Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.039516519000E+02 against expected result 2.039517E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.039520000000E+02 against expected result 2.039520E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006540000000E+02 against expected result 1.006540E+02 *** PASSED *** Testing computed result 1.994930000000E+02 against expected result 1.994930E+02 *** PASSED *** Testing computed result 4.430144947418E+00 against expected result 4.430145E+00 *** PASSED *** Elapsed time: 0.363949 seconds -------------------------------------------------------------------------------- Total elapsed time: 1.485212 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for solv section -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermidiate energies in input file apbs-mol.out Testing computed result 1.847663548071E+03 against expected result 1.847664E+03 *** PASSED *** Testing computed result 1.883912182952E+03 against expected result 1.883912E+03 *** PASSED *** Testing computed result 2.732623683321E+03 against expected result 2.732624E+03 *** PASSED *** Testing computed result 3.123035854133E+03 against expected result 3.123036E+03 *** PASSED *** Testing computed result -3.624863488075E+01 against expected result -3.624863E+01 *** PASSED *** Testing computed result -3.904121708125E+02 against expected result -3.904121E+02 *** PASSED *** Testing computed result -3.541635359318E+02 against expected result -3.541635E+02 *** PASSED *** Elapsed time: 0.523387 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermidiate energies in input file apbs-smol.out Testing computed result 1.847860440020E+03 against expected result 1.847860E+03 *** PASSED *** Testing computed result 1.885436377745E+03 against expected result 1.885436E+03 *** PASSED *** Testing computed result 2.734040568569E+03 against expected result 2.734041E+03 *** PASSED *** Testing computed result 3.125279428954E+03 against expected result 3.125279E+03 *** PASSED *** Testing computed result -3.757593772492E+01 against expected result -3.757594E+01 *** PASSED *** Testing computed result -3.912388603848E+02 against expected result -3.912388E+02 *** PASSED *** Testing computed result -3.536629226599E+02 against expected result -3.536629E+02 *** PASSED *** Elapsed time: 0.577650 seconds -------------------------------------------------------------------------------- Total elapsed time: 1.101037 seconds Test results have been loggedCreating file now: apbs-0.025.in Creating file now: apbs-0.050.in Creating file now: apbs-0.075.in Creating file now: apbs-0.100.in Creating file now: apbs-0.125.in Creating file now: apbs-0.150.in Creating file now: apbs-0.175.in Creating file now: apbs-0.200.in Creating file now: apbs-0.225.in Creating file now: apbs-0.250.in Creating file now: apbs-0.275.in Creating file now: apbs-0.300.in Creating file now: apbs-0.325.in Creating file now: apbs-0.400.in Creating file now: apbs-0.500.in Creating file now: apbs-0.600.in Creating file now: apbs-0.700.in Creating file now: apbs-0.800.in Creating file_2 now: dxmath-0.025.in Creating file_2 now: dxmath-0.050.in Creating file_2 now: dxmath-0.075.in Creating file_2 now: dxmath-0.100.in Creating file_2 now: dxmath-0.125.in Creating file_2 now: dxmath-0.150.in Creating file_2 now: dxmath-0.175.in Creating file_2 now: dxmath-0.200.in Creating file_2 now: dxmath-0.225.in Creating file_2 now: dxmath-0.250.in Creating file_2 now: dxmath-0.275.in Creating file_2 now: dxmath-0.300.in Creating file_2 now: dxmath-0.325.in Creating file_2 now: dxmath-0.400.in Creating file_2 now: dxmath-0.500.in Creating file_2 now: dxmath-0.600.in Creating file_2 now: dxmath-0.700.in Creating file_2 now: dxmath-0.800.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.025.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.186122223752E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.025.dx Ion number density to be written to ndens-complex-0.025.dx Total electrostatic energy = 3.662855899462E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.025-PE0.dx Writing number density to ndens-complex-0.025-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.477786964834E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.025.dx Ion number density to be written to ndens-pep-0.025.dx Total electrostatic energy = 1.000545153104E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.025-PE0.dx Writing number density to ndens-pep-0.025-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.329205982055E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.025.dx Ion number density to be written to ndens-rna-0.025.dx Total electrostatic energy = 2.653636629928E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.025-PE0.dx Writing number density to ndens-rna-0.025-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 8.674116429344E+01 kJ/mol Global net ELEC energy = 8.674116429344E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.050.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.184763478312E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.050.dx Ion number density to be written to ndens-complex-0.050.dx Total electrostatic energy = 3.661493366846E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.050-PE0.dx Writing number density to ndens-complex-0.050-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.475252516617E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.050.dx Ion number density to be written to ndens-pep-0.050.dx Total electrostatic energy = 1.000292179294E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.050-PE0.dx Writing number density to ndens-pep-0.050-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.327168361816E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.050.dx Ion number density to be written to ndens-rna-0.050.dx Total electrostatic energy = 2.651594350839E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.050-PE0.dx Writing number density to ndens-rna-0.050-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 9.606836713876E+01 kJ/mol Global net ELEC energy = 9.606836713876E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.075.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.184033569905E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.075.dx Ion number density to be written to ndens-complex-0.075.dx Total electrostatic energy = 3.660761530545E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.075-PE0.dx Writing number density to ndens-complex-0.075-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.473669396547E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.075.dx Ion number density to be written to ndens-pep-0.075.dx Total electrostatic energy = 1.000134276339E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.075-PE0.dx Writing number density to ndens-pep-0.075-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.326088212207E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.075.dx Ion number density to be written to ndens-rna-0.075.dx Total electrostatic energy = 2.650511882057E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.075-PE0.dx Writing number density to ndens-rna-0.075-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.011537214883E+02 kJ/mol Global net ELEC energy = 1.011537214883E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.100.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.183548000794E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.100.dx Ion number density to be written to ndens-complex-0.100.dx Total electrostatic energy = 3.660274809589E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.100-PE0.dx Writing number density to ndens-complex-0.100-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.472507235893E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.100.dx Ion number density to be written to ndens-pep-0.100.dx Total electrostatic energy = 1.000018407412E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.100-PE0.dx Writing number density to ndens-pep-0.100-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.325372656922E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.100.dx Ion number density to be written to ndens-rna-0.100.dx Total electrostatic energy = 2.649794981016E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.100-PE0.dx Writing number density to ndens-rna-0.100-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.046142116108E+02 kJ/mol Global net ELEC energy = 1.046142116108E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.125.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.183190100647E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.125.dx Ion number density to be written to ndens-complex-0.125.dx Total electrostatic energy = 3.659916161996E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.125-PE0.dx Writing number density to ndens-complex-0.125-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.471585837513E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.125.dx Ion number density to be written to ndens-pep-0.125.dx Total electrostatic energy = 9.999265654586E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.125-PE0.dx Writing number density to ndens-pep-0.125-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.324845847155E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.125.dx Ion number density to be written to ndens-rna-0.125.dx Total electrostatic energy = 2.649267328362E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.125-PE0.dx Writing number density to ndens-rna-0.125-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.072226817610E+02 kJ/mol Global net ELEC energy = 1.072226817610E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.150.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182909678356E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.150.dx Ion number density to be written to ndens-complex-0.150.dx Total electrostatic energy = 3.659635228953E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.150-PE0.dx Writing number density to ndens-complex-0.150-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.470821300868E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.150.dx Ion number density to be written to ndens-pep-0.150.dx Total electrostatic energy = 9.998503715551E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.150-PE0.dx Writing number density to ndens-pep-0.150-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.324433086171E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.150.dx Ion number density to be written to ndens-rna-0.150.dx Total electrostatic energy = 2.648854016160E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.150-PE0.dx Writing number density to ndens-rna-0.150-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.093084123762E+02 kJ/mol Global net ELEC energy = 1.093084123762E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.175.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182680817429E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.175.dx Ion number density to be written to ndens-complex-0.175.dx Total electrostatic energy = 3.659406006570E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.175-PE0.dx Writing number density to ndens-complex-0.175-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.470167484600E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.175.dx Ion number density to be written to ndens-pep-0.175.dx Total electrostatic energy = 9.997852199372E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.175-PE0.dx Writing number density to ndens-pep-0.175-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.324096101131E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.175.dx Ion number density to be written to ndens-rna-0.175.dx Total electrostatic energy = 2.648516662194E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.175-PE0.dx Writing number density to ndens-rna-0.175-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.110412443878E+02 kJ/mol Global net ELEC energy = 1.110412443878E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.200.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182488501939E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.200.dx Ion number density to be written to ndens-complex-0.200.dx Total electrostatic energy = 3.659213428941E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.200-PE0.dx Writing number density to ndens-complex-0.200-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.469596195763E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.200.dx Ion number density to be written to ndens-pep-0.200.dx Total electrostatic energy = 9.997282974485E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.200-PE0.dx Writing number density to ndens-pep-0.200-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323812822097E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.200.dx Ion number density to be written to ndens-rna-0.200.dx Total electrostatic energy = 2.648233134327E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.200-PE0.dx Writing number density to ndens-rna-0.200-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.125199716537E+02 kJ/mol Global net ELEC energy = 1.125199716537E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.225.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182323306491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.225.dx Ion number density to be written to ndens-complex-0.225.dx Total electrostatic energy = 3.659048040133E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.225-PE0.dx Writing number density to ndens-complex-0.225-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.469088900775E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.225.dx Ion number density to be written to ndens-pep-0.225.dx Total electrostatic energy = 9.996777552566E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.225-PE0.dx Writing number density to ndens-pep-0.225-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323569434544E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.225.dx Ion number density to be written to ndens-rna-0.225.dx Total electrostatic energy = 2.647989580221E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.225-PE0.dx Writing number density to ndens-rna-0.225-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.138070465620E+02 kJ/mol Global net ELEC energy = 1.138070465620E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! -------------------------------------------------------------------------------- Running tests for protein-rna section -------------------------------------------------------------------------------- Testing input file apbs-0.025.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.186122223752E+04 against expected result 3.186122E+04 *** PASSED *** Testing computed result 3.662855899462E+04 against expected result 3.662856E+04 *** PASSED *** Testing computed result 8.477786964834E+03 against expected result 8.477787E+03 *** PASSED *** Testing computed result 1.000545153104E+04 against expected result 1.000545E+04 *** PASSED *** Testing computed result 2.329205982055E+04 against expected result 2.329206E+04 *** PASSED *** Testing computed result 2.653636629928E+04 against expected result 2.653637E+04 *** PASSED *** Testing computed result 8.674116429344E+01 against expected result 8.674116E+01 *** PASSED *** Elapsed time: 9.574080 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.050.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.184763478312E+04 against expected result 3.184763E+04 *** PASSED *** Testing computed result 3.661493366846E+04 against expected result 3.661493E+04 *** PASSED *** Testing computed result 8.475252516617E+03 against expected result 8.475253E+03 *** PASSED *** Testing computed result 1.000292179294E+04 against expected result 1.000292E+04 *** PASSED *** Testing computed result 2.327168361816E+04 against expected result 2.327168E+04 *** PASSED *** Testing computed result 2.651594350839E+04 against expected result 2.651594E+04 *** PASSED *** Testing computed result 9.606836713876E+01 against expected result 9.606837E+01 *** PASSED *** Elapsed time: 9.588214 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.075.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.184033569905E+04 against expected result 3.184034E+04 *** PASSED *** Testing computed result 3.660761530545E+04 against expected result 3.660762E+04 *** PASSED *** Testing computed result 8.473669396547E+03 against expected result 8.473669E+03 *** PASSED *** Testing computed result 1.000134276339E+04 against expected result 1.000134E+04 *** PASSED *** Testing computed result 2.326088212207E+04 against expected result 2.326088E+04 *** PASSED *** Testing computed result 2.650511882057E+04 against expected result 2.650512E+04 *** PASSED *** Testing computed result 1.011537214883E+02 against expected result 1.011537E+02 *** PASSED *** Elapsed time: 9.442126 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.100.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.183548000794E+04 against expected result 3.183548E+04 *** PASSED *** Testing computed result 3.660274809589E+04 against expected result 3.660275E+04 *** PASSED *** Testing computed result 8.472507235893E+03 against expected result 8.472507E+03 *** PASSED *** Testing computed result 1.000018407412E+04 against expected result 1.000018E+04 *** PASSED *** Testing computed result 2.325372656922E+04 against expected result 2.325373E+04 *** PASSED *** Testing computed result 2.649794981016E+04 against expected result 2.649795E+04 *** PASSED *** Testing computed result 1.046142116108E+02 against expected result 1.046142E+02 *** PASSED *** Elapsed time: 9.677804 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.125.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.183190100647E+04 against expected result 3.183190E+04 *** PASSED *** Testing computed result 3.659916161996E+04 against expected result 3.659916E+04 *** PASSED *** Testing computed result 8.471585837513E+03 against expected result 8.471586E+03 *** PASSED *** Testing computed result 9.999265654586E+03 against expected result 9.999266E+03 *** PASSED *** Testing computed result 2.324845847155E+04 against expected result 2.324846E+04 *** PASSED *** Testing computed result 2.649267328362E+04 against expected result 2.649267E+04 *** PASSED *** Testing computed result 1.072226817610E+02 against expected result 1.072227E+02 *** PASSED *** Elapsed time: 9.613026 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.150.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.182909678356E+04 against expected result 3.182910E+04 *** PASSED *** Testing computed result 3.659635228953E+04 against expected result 3.659635E+04 *** PASSED *** Testing computed result 8.470821300868E+03 against expected result 8.470821E+03 *** PASSED *** Testing computed result 9.998503715551E+03 against expected result 9.998504E+03 *** PASSED *** Testing computed result 2.324433086171E+04 against expected result 2.324433E+04 *** PASSED *** Testing computed result 2.648854016160E+04 against expected result 2.648854E+04 *** PASSED *** Testing computed result 1.093084123762E+02 against expected result 1.093084E+02 *** PASSED *** Elapsed time: 9.733858 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.175.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.182680817429E+04 against expected result 3.182681E+04 *** PASSED *** Testing computed result 3.659406006570E+04 against expected result 3.659406E+04 *** PASSED *** Testing computed result 8.470167484600E+03 against expected result 8.470167E+03 *** PASSED *** Testing computed result 9.997852199372E+03 against expected result 9.997852E+03 *** PASSED *** Testing computed result 2.324096101131E+04 against expected result 2.324096E+04 *** PASSED *** Testing computed result 2.648516662194E+04 against expected result 2.648517E+04 *** PASSED *** Testing computed result 1.110412443878E+02 against expected result 1.110412E+02 *** PASSED *** Elapsed time: 9.671178 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.200.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.182488501939E+04 against expected result 3.182489E+04 *** PASSED *** Testing computed result 3.659213428941E+04 against expected result 3.659213E+04 *** PASSED *** Testing computed result 8.469596195763E+03 against expected result 8.469596E+03 *** PASSED *** Testing computed result 9.997282974485E+03 against expected result 9.997283E+03 *** PASSED *** Testing computed result 2.323812822097E+04 against expected result 2.323813E+04 *** PASSED *** Testing computed result 2.648233134327E+04 against expected result 2.648233E+04 *** PASSED *** Testing computed result 1.125199716537E+02 against expected result 1.125200E+02 *** PASSED *** Elapsed time: 9.857862 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.225.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.182323306491E+04 against expected result 3.182323E+04 *** PASSED *** Testing computed result 3.659048040133E+04 against expected result 3.659048E+04 *** PASSED *** Testing computed result 8.469088900775E+03 against expected result 8.469089E+03 *** PASSED ***asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.250.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182178954360E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.250.dx Ion number density to be written to ndens-complex-0.250.dx Total electrostatic energy = 3.658903543806E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.250-PE0.dx Writing number density to ndens-complex-0.250-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.468632740499E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.250.dx Ion number density to be written to ndens-pep-0.250.dx Total electrostatic energy = 9.996323108319E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.250-PE0.dx Writing number density to ndens-pep-0.250-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323356752071E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.250.dx Ion number density to be written to ndens-rna-0.250.dx Total electrostatic energy = 2.647776789284E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.250-PE0.dx Writing number density to ndens-rna-0.250-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.149444369079E+02 kJ/mol Global net ELEC energy = 1.149444369079E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.275.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182051070674E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.275.dx Ion number density to be written to ndens-complex-0.275.dx Total electrostatic energy = 3.658775551975E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.275-PE0.dx Writing number density to ndens-complex-0.275-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.468218414737E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.275.dx Ion number density to be written to ndens-pep-0.275.dx Total electrostatic energy = 9.995910367297E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.275-PE0.dx Writing number density to ndens-pep-0.275-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323168374787E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.275.dx Ion number density to be written to ndens-rna-0.275.dx Total electrostatic energy = 2.647588345522E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.275-PE0.dx Writing number density to ndens-rna-0.275-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.159616972339E+02 kJ/mol Global net ELEC energy = 1.159616972339E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.300.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181936493519E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.300.dx Ion number density to be written to ndens-complex-0.300.dx Total electrostatic energy = 3.658660893678E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.300-PE0.dx Writing number density to ndens-complex-0.300-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.467838971928E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.300.dx Ion number density to be written to ndens-pep-0.300.dx Total electrostatic energy = 9.995532397856E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.300-PE0.dx Writing number density to ndens-pep-0.300-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322999676177E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.300.dx Ion number density to be written to ndens-rna-0.300.dx Total electrostatic energy = 2.647419611346E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.300-PE0.dx Writing number density to ndens-rna-0.300-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.168804254686E+02 kJ/mol Global net ELEC energy = 1.168804254686E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.325.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181832869046E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.325.dx Ion number density to be written to ndens-complex-0.325.dx Total electrostatic energy = 3.658557208654E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.325-PE0.dx Writing number density to ndens-complex-0.325-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.467489074881E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.325.dx Ion number density to be written to ndens-pep-0.325.dx Total electrostatic energy = 9.995183878464E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.325-PE0.dx Writing number density to ndens-pep-0.325-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322847209567E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.325.dx Ion number density to be written to ndens-rna-0.325.dx Total electrostatic energy = 2.647267132259E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.325-PE0.dx Writing number density to ndens-rna-0.325-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.177168854907E+02 kJ/mol Global net ELEC energy = 1.177168854907E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.400.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181571629593E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.400.dx Ion number density to be written to ndens-complex-0.400.dx Total electrostatic energy = 3.658295870300E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.400-PE0.dx Writing number density to ndens-complex-0.400-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.466578740909E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.400.dx Ion number density to be written to ndens-pep-0.400.dx Total electrostatic energy = 9.994277216885E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.400-PE0.dx Writing number density to ndens-pep-0.400-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322463613929E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.400.dx Ion number density to be written to ndens-rna-0.400.dx Total electrostatic energy = 2.646883588223E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.400-PE0.dx Writing number density to ndens-rna-0.400-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.198456038803E+02 kJ/mol Global net ELEC energy = 1.198456038803E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.500.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181302243781E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.500.dx Ion number density to be written to ndens-complex-0.500.dx Total electrostatic energy = 3.658026461575E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.500-PE0.dx Writing number density to ndens-complex-0.500-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.465598755475E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.500.dx Ion number density to be written to ndens-pep-0.500.dx Total electrostatic energy = 9.993301332440E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.500-PE0.dx Writing number density to ndens-pep-0.500-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322070101887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.500.dx Ion number density to be written to ndens-rna-0.500.dx Total electrostatic energy = 2.646490251594E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.500-PE0.dx Writing number density to ndens-rna-0.500-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.220607673699E+02 kJ/mol Global net ELEC energy = 1.220607673699E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.600.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181090090954E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.600.dx Ion number density to be written to ndens-complex-0.600.dx Total electrostatic energy = 3.657814345443E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.600-PE0.dx Writing number density to ndens-complex-0.600-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.464799341688E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.600.dx Ion number density to be written to ndens-pep-0.600.dx Total electrostatic energy = 9.992505379555E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.600-PE0.dx Writing number density to ndens-pep-0.600-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.321762631365E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.600.dx Ion number density to be written to ndens-rna-0.600.dx Total electrostatic energy = 2.646183001839E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.600-PE0.dx Writing number density to ndens-rna-0.600-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.238080564885E+02 kJ/mol Global net ELEC energy = 1.238080564885E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.700.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.180915789156E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.700.dx Ion number density to be written to ndens-complex-0.700.dx Total electrostatic energy = 3.657640108752E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.700-PE0.dx Writing number density to ndens-complex-0.700-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.464126109756E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.700.dx Ion number density to be written to ndens-pep-0.700.dx Total electrostatic energy = 9.991835140855E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.700-PE0.dx Writing number density to ndens-pep-0.700-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.321512352191E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.700.dx Ion number density to be written to ndens-rna-0.700.dx Total electrostatic energy = 2.645932953757E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.700-PE0.dx Writing number density to ndens-rna-0.700-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.252364090878E+02 kJ/mol Global net ELEC energy = 1.252364090878E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! Testing computed result 9.996777552566E+03 against expected result 9.996778E+03 *** PASSED *** Testing computed result 2.323569434544E+04 against expected result 2.323569E+04 *** PASSED *** Testing computed result 2.647989580221E+04 against expected result 2.647990E+04 *** PASSED *** Testing computed result 1.138070465620E+02 against expected result 1.138070E+02 *** PASSED *** Elapsed time: 9.791691 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.250.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.182178954360E+04 against expected result 3.182179E+04 *** PASSED *** Testing computed result 3.658903543806E+04 against expected result 3.658904E+04 *** PASSED *** Testing computed result 8.468632740499E+03 against expected result 8.468633E+03 *** PASSED *** Testing computed result 9.996323108319E+03 against expected result 9.996323E+03 *** PASSED *** Testing computed result 2.323356752071E+04 against expected result 2.323357E+04 *** PASSED *** Testing computed result 2.647776789284E+04 against expected result 2.647777E+04 *** PASSED *** Testing computed result 1.149444369079E+02 against expected result 1.149444E+02 *** PASSED *** Elapsed time: 9.709633 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.275.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.182051070674E+04 against expected result 3.182051E+04 *** PASSED *** Testing computed result 3.658775551975E+04 against expected result 3.658776E+04 *** PASSED *** Testing computed result 8.468218414737E+03 against expected result 8.468218E+03 *** PASSED *** Testing computed result 9.995910367297E+03 against expected result 9.995910E+03 *** PASSED *** Testing computed result 2.323168374787E+04 against expected result 2.323168E+04 *** PASSED *** Testing computed result 2.647588345522E+04 against expected result 2.647588E+04 *** PASSED *** Testing computed result 1.159616972339E+02 against expected result 1.159617E+02 *** PASSED *** Elapsed time: 9.926451 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.300.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.181936493519E+04 against expected result 3.181936E+04 *** PASSED *** Testing computed result 3.658660893678E+04 against expected result 3.658661E+04 *** PASSED *** Testing computed result 8.467838971928E+03 against expected result 8.467839E+03 *** PASSED *** Testing computed result 9.995532397856E+03 against expected result 9.995532E+03 *** PASSED *** Testing computed result 2.322999676177E+04 against expected result 2.323000E+04 *** PASSED *** Testing computed result 2.647419611346E+04 against expected result 2.647420E+04 *** PASSED *** Testing computed result 1.168804254686E+02 against expected result 1.168804E+02 *** PASSED *** Elapsed time: 9.727563 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.325.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.181832869046E+04 against expected result 3.181833E+04 *** PASSED *** Testing computed result 3.658557208654E+04 against expected result 3.658557E+04 *** PASSED *** Testing computed result 8.467489074881E+03 against expected result 8.467489E+03 *** PASSED *** Testing computed result 9.995183878464E+03 against expected result 9.995184E+03 *** PASSED *** Testing computed result 2.322847209567E+04 against expected result 2.322847E+04 *** PASSED *** Testing computed result 2.647267132259E+04 against expected result 2.647267E+04 *** PASSED *** Testing computed result 1.177168854907E+02 against expected result 1.177169E+02 *** PASSED *** Elapsed time: 9.748125 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.400.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.181571629593E+04 against expected result 3.181572E+04 *** PASSED *** Testing computed result 3.658295870300E+04 against expected result 3.658296E+04 *** PASSED *** Testing computed result 8.466578740909E+03 against expected result 8.466579E+03 *** PASSED *** Testing computed result 9.994277216885E+03 against expected result 9.994277E+03 *** PASSED *** Testing computed result 2.322463613929E+04 against expected result 2.322464E+04 *** PASSED *** Testing computed result 2.646883588223E+04 against expected result 2.646884E+04 *** PASSED *** Testing computed result 1.198456038803E+02 against expected result 1.198456E+02 *** PASSED *** Elapsed time: 9.760401 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.500.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.181302243781E+04 against expected result 3.181302E+04 *** PASSED *** Testing computed result 3.658026461575E+04 against expected result 3.658026E+04 *** PASSED *** Testing computed result 8.465598755475E+03 against expected result 8.465599E+03 *** PASSED *** Testing computed result 9.993301332440E+03 against expected result 9.993301E+03 *** PASSED *** Testing computed result 2.322070101887E+04 against expected result 2.322070E+04 *** PASSED *** Testing computed result 2.646490251594E+04 against expected result 2.646490E+04 *** PASSED *** Testing computed result 1.220607673699E+02 against expected result 1.220608E+02 *** PASSED *** Elapsed time: 9.512219 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.600.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.181090090954E+04 against expected result 3.181090E+04 *** PASSED *** Testing computed result 3.657814345443E+04 against expected result 3.657814E+04 *** PASSED *** Testing computed result 8.464799341688E+03 against expected result 8.464799E+03 *** PASSED *** Testing computed result 9.992505379555E+03 against expected result 9.992505E+03 *** PASSED *** Testing computed result 2.321762631365E+04 against expected result 2.321763E+04 *** PASSED *** Testing computed result 2.646183001839E+04 against expected result 2.646183E+04 *** PASSED *** Testing computed result 1.238080564885E+02 against expected result 1.238081E+02 *** PASSED *** Elapsed time: 9.576787 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.700.in Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.180915789156E+04 against expected result 3.180916E+04 *** PASSED *** Testing computed result 3.657640108752E+04 against expected result 3.657640E+04 *** PASSED *** Testing computed result 8.464126109756E+03 against expected result 8.464126E+03 *** PASSED *** Testing computed result 9.991835140855E+03 against expected result 9.991835E+03 *** PASSED *** Testing computed result 2.321512352191E+04 against expected result 2.321512E+04 *** PASSED *** Testing computed result 2.645932953757E+04 against expected result 2.645933E+04 *** PASSED *** Testing computed result 1.252364090878E+02 against expected result 1.252364E+02 *** PASSED *** Elapsed time: 9.621088 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.800.inasc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 1.5 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Apr 3 2020 at 04:05:58 Parsing input file apbs-0.800.in... rank 0 size 1... read Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 215.806 MB total, 215.806 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.180768241803E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 215.806 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.800.dx Ion number density to be written to ndens-complex-0.800.dx Total electrostatic energy = 3.657492640520E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.800-PE0.dx Writing number density to ndens-complex-0.800-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.463546035019E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 200.170 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.800.dx Ion number density to be written to ndens-pep-0.800.dx Total electrostatic energy = 9.991257699113E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.800-PE0.dx Writing number density to ndens-pep-0.800-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.321302636223E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 208.532 MB total, 428.131 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.800.dx Ion number density to be written to ndens-rna-0.800.dx Total electrostatic energy = 2.645723464562E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.800-PE0.dx Writing number density to ndens-rna-0.800-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.264340604647E+02 kJ/mol Global net ELEC energy = 1.264340604647E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.131 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out Testing computed result 3.180768241803E+04 against expected result 3.180768E+04 *** PASSED *** Testing computed result 3.657492640520E+04 against expected result 3.657493E+04 *** PASSED *** Testing computed result 8.463546035019E+03 against expected result 8.463546E+03 *** PASSED *** Testing computed result 9.991257699113E+03 against expected result 9.991258E+03 *** PASSED *** Testing computed result 2.321302636223E+04 against expected result 2.321303E+04 *** PASSED *** Testing computed result 2.645723464562E+04 against expected result 2.645723E+04 *** PASSED *** Testing computed result 1.264340604647E+02 against expected result 1.264341E+02 *** PASSED *** Elapsed time: 9.628927 seconds -------------------------------------------------------------------------------- Total elapsed time: 174.161033 seconds Test results have been logged -------------------------------------------------------------------------------- make[1]: Leaving directory '/<>/apbs-1.5+dfsg1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3 dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>/apbs-1.5+dfsg1' dh_auto_install --sourcedir=apbs --destdir=/<>/apbs-1.5+dfsg1/debian/tmp/ cd obj-s390x-linux-gnu && make -j4 install DESTDIR=/<>/apbs-1.5\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' /usr/bin/cmake -S/<>/apbs-1.5+dfsg1/apbs -B/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/CMakeFiles /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src/pmgc /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake --color= cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src/generic /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/python/CMakeFiles/apbslib_swig_compilation.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'src/generic/CMakeFiles/apbs_generic.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'src/pmgc/CMakeFiles/apbs_pmgc.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 1%] Built target apbslib_swig_compilation [ 23%] Built target apbs_generic [ 45%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src/mg /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'src/mg/CMakeFiles/apbs_mg.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 52%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'src/CMakeFiles/apbs_routines.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build [ 54%] Built target apbs_routines make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/tensor2dx.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 56%] Built target uhbd_asc2bin make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/mgmesh.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake --color= [ 59%] Built target tensor2dx make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend [ 61%] Built target mgmesh make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/mergedx.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/mergedx2.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/build [ 63%] Built target mergedx make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake --color= make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/del2dx.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/analysis.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 66%] Built target mergedx2 make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend [ 68%] Built target del2dx make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/value.dir/DependInfo.cmake --color= [ 70%] Built target analysis make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/similarity.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/dxmath.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/benchmark.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/value.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/build [ 73%] Built target dxmath make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/similarity.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake --color= [ 75%] Built target benchmark [ 77%] Built target value make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend [ 80%] Built target similarity make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/mesh/CMakeFiles/dx2uhbd.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/dx2mol.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/multivalue.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/smooth.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 82%] Built target dx2mol make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/mesh/CMakeFiles/dx2uhbd.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake --color= [ 86%] Built target multivalue [ 87%] Built target dx2uhbd make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake --color= [ 89%] Built target smooth make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/manip/CMakeFiles/born.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' cd /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs-1.5+dfsg1/apbs /<>/apbs-1.5+dfsg1/apbs/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/manip/CMakeFiles/coulomb.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 91%] Built target born make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build [ 94%] Built target coulomb make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'tools/python/CMakeFiles/_apbslib.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[4]: Nothing to be done for 'src/CMakeFiles/apbs.dir/build'. make[4]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' [ 96%] Built target _apbslib [100%] Built target apbs make[3]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_128_v2.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_16.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_512.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_64.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_1024.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_32.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_256.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/icons/APBS_128.png -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/ChangeLog.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/README -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/license -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/license/license.html -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/license/LICENSE.txt -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/release_procedure.txt -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/data-ontology -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/data-ontology/data-ontology.ttl -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/data-ontology/catalog-v001.xml -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/data-ontology/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/data-ontology/protege.sh -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/doc/ReleaseNotes.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/mesh.m -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/hca.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/io.mc -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.log -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/hca-bind/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/ASP66.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/491.pdb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.pdb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.inp -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/membrane -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/membrane/readme.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/membrane/pot.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/membrane/memv.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/io.mc -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -- 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/<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbam/1a63.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbam/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbam/1a63.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.out -- Installing: 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-- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ionize -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr -- Installing: 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/<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/io.mc -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/Makefile.am -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/UHBD -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.inp.exam -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam -- Installing: 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/<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.out -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/io.mc -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/Makefile.in -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/README.md -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/examples/alkanes/force.result -- Installing: 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/<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/value.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/analysis.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/smooth.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/dx2mol.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/similarity.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/mgmesh.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/tensor2dx.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/mgmesh -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_routines.so.1 -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_routines.so -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/apbs.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/routines.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/bin/apbs -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/nosh.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/mgparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/femparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/pbamparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/pbsamparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/pbeparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/bemparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/geoflowparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/apolparm.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vacc.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/valist.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vatom.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vpbe.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vcap.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vclist.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vstring.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vparam.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vgreen.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vmatrix.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vhal.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/generic/vunit.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_generic.so.1 -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_generic.so -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/buildAd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/buildBd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/buildGd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/buildPd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/cgd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/gsd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/matvecd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/mgcsd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/mgdrvd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/mgsubd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/mikpckd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/mlinpckd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/mypdec.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/newtond.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/newdrvd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/powerd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/smoothd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/pmgc/mgfasd.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_pmgc.so.1 -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_pmgc.so -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/mg/vgrid.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/mg/vmgrid.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/mg/vopot.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/mg/vpmg.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/include/apbs/mg/vpmgp.h -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_mg.so.1 -- Installing: /<>/apbs-1.5+dfsg1/debian/tmp/usr/lib/s390x-linux-gnu/libapbs_mg.so make[2]: Leaving directory '/<>/apbs-1.5+dfsg1/obj-s390x-linux-gnu' make[1]: Leaving directory '/<>/apbs-1.5+dfsg1' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_python3 -a I: dh_python3 fs:343: renaming _apbslib.so to _apbslib.cpython-38-s390x-linux-gnu.so dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_missing: warning: usr/share/apbs/tools/README.html exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/pot.net exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/potacc.net exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/potacc.cfg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/pot.cm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/surface.net exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/multipot.cfg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/multipot.net exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/surface.cfg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/potacc.cm exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/visualization/opendx/pot.cfg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/manip/__pycache__/inputgen.cpython-38.pyc exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/tools/manip/__pycache__/psize.cpython-38.pyc exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/release_procedure.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_128_v2.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_16.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_512.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_64.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_1024.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_32.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_256.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/icons/APBS_128.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/license/license.html exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/license/LICENSE.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/data-ontology/data-ontology.ttl exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/data-ontology/catalog-v001.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/data-ontology/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/apbs/doc/data-ontology/protege.sh exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: apbs (2), apbs-data (7), libapbs-dev (5), libapbs1 (4), python3-apbslib (4) * dh_installdocs: apbs (4), apbs-data (0), libapbs-dev (3), libapbs1 (0), python3-apbslib (0) * dh_installman: apbs (1), apbs-data (0), libapbs-dev (0), libapbs1 (0), python3-apbslib (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built For a short-term work-around: Add the files to debian/not-installed dh_dwz -a dwz: debian/libapbs1/usr/lib/s390x-linux-gnu/libapbs_pmgc.so.1: DWARF compression not beneficial - old size 154706 new size 154789 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libapbs1/usr/lib/s390x-linux-gnu/libapbs_generic.so.1 was not linked against libpthread.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd were not linked against libapbs_pmgc.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd were not linked against libmpi.so.40 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs was not linked against libapbs_routines.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd were not linked against libpthread.so.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd were not linked against libgomp.so.1 (they use none of the library's symbols) dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing apbs (in debian/apbs); do_strip: , oemstrip: pkgstriptranslations: processing python3-apbslib (in debian/python3-apbslib); do_strip: , oemstrip: pkgstriptranslations: processing libapbs1-dbgsym (in debian/.debhelper/libapbs1/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libapbs-dev (in debian/libapbs-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-apbslib/DEBIAN/control, package python3-apbslib, directory debian/python3-apbslib INFO: pkgstripfiles: waiting for lock (python3-apbslib) ... pkgstripfiles: processing control file: debian/apbs/DEBIAN/control, package apbs, directory debian/apbs .. removing usr/share/doc/apbs/ChangeLog.md Searching for duplicated docs in dependency libapbs1... pkgstripfiles: processing control file: debian/.debhelper/libapbs1/dbgsym-root/DEBIAN/control, package libapbs1-dbgsym, directory debian/.debhelper/libapbs1/dbgsym-root dpkg-deb: building package 'libapbs1-dbgsym' in 'debian/.debhelper/scratch-space/build-libapbs1/libapbs1-dbgsym_1.5+dfsg1-3_s390x.deb'. symlinking changelog.Debian.gz in apbs to file in libapbs1 pkgstripfiles: Running PNG optimization (using 4 cpus) for package apbs ... pkgstripfiles: No PNG files. dpkg-deb: building package 'apbs' in '../apbs_1.5+dfsg1-3_s390x.deb'. Renaming libapbs1-dbgsym_1.5+dfsg1-3_s390x.deb to libapbs1-dbgsym_1.5+dfsg1-3_s390x.ddeb INFO: pkgstriptranslations version 144 pkgstriptranslations: processing apbs-dbgsym (in debian/.debhelper/apbs/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/apbs/dbgsym-root/DEBIAN/control, package apbs-dbgsym, directory debian/.debhelper/apbs/dbgsym-root dpkg-deb: building package 'apbs-dbgsym' in 'debian/.debhelper/scratch-space/build-apbs/apbs-dbgsym_1.5+dfsg1-3_s390x.deb'. Renaming apbs-dbgsym_1.5+dfsg1-3_s390x.deb to apbs-dbgsym_1.5+dfsg1-3_s390x.ddeb Searching for duplicated docs in dependency libapbs1... symlinking changelog.Debian.gz in python3-apbslib to file in libapbs1 pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-apbslib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_1.5+dfsg1-3_s390x.deb'. 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Renaming python3-apbslib-dbgsym_1.5+dfsg1-3_s390x.deb to python3-apbslib-dbgsym_1.5+dfsg1-3_s390x.ddeb pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libapbs-dev/DEBIAN/control, package libapbs-dev, directory debian/libapbs-dev .. removing usr/share/doc/libapbs-dev/ChangeLog.md Searching for duplicated docs in dependency libapbs1... symlinking changelog.Debian.gz in libapbs-dev to file in libapbs1 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_1.5+dfsg1-3_s390x.deb'. INFO: pkgstriptranslations version 144 pkgstriptranslations: processing libapbs1 (in debian/libapbs1); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libapbs1/DEBIAN/control, package libapbs1, directory debian/libapbs1 pkgstripfiles: Truncating usr/share/doc/libapbs1/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs1 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs1' in '../libapbs1_1.5+dfsg1-3_s390x.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../apbs_1.5+dfsg1-3_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200508-0446 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ apbs_1.5+dfsg1-3_s390x.changes: ------------------------------- Format: 1.8 Date: Fri, 03 Apr 2020 12:05:58 +0800 Source: apbs Binary: apbs libapbs-dev libapbs1 python3-apbslib Architecture: s390x Version: 1.5+dfsg1-3 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Drew Parsons Description: apbs - Adaptive Poisson Boltzmann Solver libapbs-dev - Adaptive Poisson Boltzmann Solver libapbs1 - Adaptive Poisson Boltzmann Solver python3-apbslib - Adaptive Poisson Boltzmann Solver Changes: apbs (1.5+dfsg1-3) unstable; urgency=medium . * Team upload. * python3.patch, wrong-path-for-interpreter.patch: use python3 as python executable for tests and scripts, fix print statements Checksums-Sha1: 775a6126b24cfdc8dbbe0502c8fca17fe4b7d629 140236 apbs-dbgsym_1.5+dfsg1-3_s390x.ddeb 4fb77aea553f580af92e3f2d3e1fe09170c2bd47 10549 apbs_1.5+dfsg1-3_s390x.buildinfo 38c863869d3a056225cb7c6ae8878ac034b4f353 71268 apbs_1.5+dfsg1-3_s390x.deb ccbd86a5b200226a7fa6a4e7d12b633da8b4fd63 59432 libapbs-dev_1.5+dfsg1-3_s390x.deb e5ebd349f3767f20d1a4ee56d2ab536f68e8844f 501564 libapbs1-dbgsym_1.5+dfsg1-3_s390x.ddeb 1776b948b4300c9347cabd5bedc8e94eca8a4e8e 202036 libapbs1_1.5+dfsg1-3_s390x.deb aca277ada369ab6f199a4b73d0a07763d00c5823 134464 python3-apbslib-dbgsym_1.5+dfsg1-3_s390x.ddeb 5e3b917cca95ec05baf1d790acf1580a7204c1f0 91244 python3-apbslib_1.5+dfsg1-3_s390x.deb Checksums-Sha256: 6dbeb27397a3fb196706712ba1ac7946e1a64c8572a9042dc0ca3fa342d3871a 140236 apbs-dbgsym_1.5+dfsg1-3_s390x.ddeb 59181806e4d14d877fad3c5fc6ed14cdb0c77b4c4fbb97f396f8023043479c0a 10549 apbs_1.5+dfsg1-3_s390x.buildinfo aca2824e34c13b43b3efb5116d04b47a8a1743f3d61f08c339a92f71e29dec79 71268 apbs_1.5+dfsg1-3_s390x.deb d23004eceee0da7870e10e4dcbd1bc88e4c44c53c36793d092868d205f3bbdb9 59432 libapbs-dev_1.5+dfsg1-3_s390x.deb 07d268f1e61df990fd9c3b53845fccdfa73f53f1108f4b5c0784b37529087bd7 501564 libapbs1-dbgsym_1.5+dfsg1-3_s390x.ddeb a0df207d0ca103d2f8d6a36dc2fa16c533b806fd506cc7b11742e467345b0160 202036 libapbs1_1.5+dfsg1-3_s390x.deb 211d9f26b82856e9dd28942ec9df5636b4fe8593d8da19b184b619a77ae88d88 134464 python3-apbslib-dbgsym_1.5+dfsg1-3_s390x.ddeb dc66e0372d7f9994d1907f1894ba6f462c558c7ed4ee1d836c34a5af49841696 91244 python3-apbslib_1.5+dfsg1-3_s390x.deb Files: 001666abb643c9ea6c4096f752c89db6 140236 debug optional apbs-dbgsym_1.5+dfsg1-3_s390x.ddeb d1521359bcc17b9d6e71d08bd1fb0b0f 10549 science optional apbs_1.5+dfsg1-3_s390x.buildinfo 7e4091cdac41b66f8191062e0030ab33 71268 science optional apbs_1.5+dfsg1-3_s390x.deb a3297892737858a70b216ad956f7edc0 59432 libdevel optional libapbs-dev_1.5+dfsg1-3_s390x.deb de8b97cf57ef1b923df41588709d0352 501564 debug optional libapbs1-dbgsym_1.5+dfsg1-3_s390x.ddeb 7fa14ad9c44baf3037f631c6ae35f166 202036 libs optional libapbs1_1.5+dfsg1-3_s390x.deb 101a4dea1e15afe0808e10ee00f15e84 134464 debug optional python3-apbslib-dbgsym_1.5+dfsg1-3_s390x.ddeb 5dbb50f64e9e2f23a8a834f5bbeb81d2 91244 python optional python3-apbslib_1.5+dfsg1-3_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ apbs_1.5+dfsg1-3_s390x.deb -------------------------- new debian package, version 2.0. size 71268 bytes: control archive=1736 bytes. 1497 bytes, 30 lines control 1614 bytes, 24 lines md5sums Package: apbs Version: 1.5+dfsg1-3 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 387 Depends: apbs-data (= 1.5+dfsg1-3), libapbs1 (= 1.5+dfsg1-3), libc6 (>= 2.29), libgomp1 (>= 4.2.1), libmaloc1 (>= 0.2-1), libopenmpi3 (>= 4.0.3), libstdc++6 (>= 4.1.1) Section: science Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. . This package contains the apbs program and utilities. drwxr-xr-x root/root 0 2020-04-03 04:05 ./ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/bin/ -rwxr-xr-x root/root 96336 2020-04-03 04:05 ./usr/bin/apbs drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/apbs/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/apbs/tools/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/ -rw-r--r-- root/root 14416 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/analysis -rw-r--r-- root/root 14416 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/benchmark -rw-r--r-- root/root 14416 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/born -rw-r--r-- root/root 14416 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/coulomb -rw-r--r-- root/root 14424 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/del2dx -rw-r--r-- root/root 10320 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/dx2mol -rw-r--r-- root/root 10320 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/dx2uhbd -rw-r--r-- root/root 18512 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/dxmath -rw-r--r-- root/root 18512 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/mergedx -rw-r--r-- root/root 22608 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/mergedx2 -rw-r--r-- root/root 10320 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/mgmesh -rw-r--r-- root/root 14416 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/multivalue -rw-r--r-- root/root 22608 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/similarity -rw-r--r-- root/root 14416 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/smooth -rw-r--r-- root/root 14424 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/tensor2dx -rw-r--r-- root/root 10320 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/uhbd_asc2bin -rw-r--r-- root/root 10320 2020-04-03 04:05 ./usr/lib/apbs/tools/bin/bin/value drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/apbs/ -rw-r--r-- root/root 270 2016-10-17 21:05 ./usr/share/doc/apbs/README -rw-r--r-- root/root 294 2020-04-03 04:05 ./usr/share/doc/apbs/README.test -rw-r--r-- root/root 805 2016-10-17 21:05 ./usr/share/doc/apbs/ReleaseNotes.md lrwxrwxrwx root/root 0 2020-04-03 04:05 ./usr/share/doc/apbs/changelog.Debian.gz -> ../libapbs1/changelog.Debian.gz -rw-r--r-- root/root 3720 2020-04-03 04:05 ./usr/share/doc/apbs/copyright drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 65 2020-04-03 04:05 ./usr/share/lintian/overrides/apbs drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/man/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/man/man1/ -rw-r--r-- root/root 835 2020-04-03 04:05 ./usr/share/man/man1/apbs.1.gz libapbs-dev_1.5+dfsg1-3_s390x.deb --------------------------------- new debian package, version 2.0. size 59432 bytes: control archive=1968 bytes. 731 bytes, 19 lines control 3250 bytes, 49 lines md5sums Package: libapbs-dev Source: apbs Version: 1.5+dfsg1-3 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 579 Depends: libapbs1 (= 1.5+dfsg1-3) Section: libdevel Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the development headers to build against libapbs_* shared libraries. drwxr-xr-x root/root 0 2020-04-03 04:05 ./ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/include/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/include/apbs/ -rw-r--r-- root/root 3322 2016-10-17 21:05 ./usr/include/apbs/apbs.h drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/include/apbs/generic/ -rw-r--r-- root/root 8229 2016-10-17 21:05 ./usr/include/apbs/generic/apolparm.h -rw-r--r-- root/root 6401 2016-10-17 21:05 ./usr/include/apbs/generic/bemparm.h -rw-r--r-- root/root 8873 2016-10-17 21:05 ./usr/include/apbs/generic/femparm.h -rw-r--r-- root/root 6121 2016-10-17 21:05 ./usr/include/apbs/generic/geoflowparm.h -rw-r--r-- root/root 12602 2016-10-17 21:05 ./usr/include/apbs/generic/mgparm.h -rw-r--r-- root/root 21063 2016-10-17 21:05 ./usr/include/apbs/generic/nosh.h -rw-r--r-- root/root 10919 2016-10-17 21:05 ./usr/include/apbs/generic/pbamparm.h 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./usr/include/apbs/generic/vstring.h -rw-r--r-- root/root 3958 2016-10-17 21:05 ./usr/include/apbs/generic/vunit.h drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/include/apbs/mg/ -rw-r--r-- root/root 14945 2016-10-17 21:05 ./usr/include/apbs/mg/vgrid.h -rw-r--r-- root/root 6887 2016-10-17 21:05 ./usr/include/apbs/mg/vmgrid.h -rw-r--r-- root/root 6160 2016-10-17 21:05 ./usr/include/apbs/mg/vopot.h -rw-r--r-- root/root 53359 2016-10-17 21:05 ./usr/include/apbs/mg/vpmg.h -rw-r--r-- root/root 11010 2016-10-17 21:05 ./usr/include/apbs/mg/vpmgp.h drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/include/apbs/pmgc/ -rw-r--r-- root/root 12319 2016-10-17 21:05 ./usr/include/apbs/pmgc/buildAd.h -rw-r--r-- root/root 5305 2016-10-17 21:05 ./usr/include/apbs/pmgc/buildBd.h -rw-r--r-- root/root 16972 2016-10-17 21:05 ./usr/include/apbs/pmgc/buildGd.h -rw-r--r-- root/root 10038 2016-10-17 21:05 ./usr/include/apbs/pmgc/buildPd.h -rw-r--r-- root/root 3475 2016-10-17 21:05 ./usr/include/apbs/pmgc/cgd.h 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-rw-r--r-- root/root 33346 2016-10-17 21:05 ./usr/include/apbs/routines.h drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/ lrwxrwxrwx root/root 0 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_generic.so -> libapbs_generic.so.1 lrwxrwxrwx root/root 0 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_mg.so -> libapbs_mg.so.1 lrwxrwxrwx root/root 0 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_pmgc.so -> libapbs_pmgc.so.1 lrwxrwxrwx root/root 0 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_routines.so -> libapbs_routines.so.1 drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/libapbs-dev/ -rw-r--r-- root/root 270 2016-10-17 21:05 ./usr/share/doc/libapbs-dev/README -rw-r--r-- root/root 805 2016-10-17 21:05 ./usr/share/doc/libapbs-dev/ReleaseNotes.md lrwxrwxrwx root/root 0 2020-04-03 04:05 ./usr/share/doc/libapbs-dev/changelog.Debian.gz -> ../libapbs1/changelog.Debian.gz -rw-r--r-- root/root 3720 2020-04-03 04:05 ./usr/share/doc/libapbs-dev/copyright libapbs1_1.5+dfsg1-3_s390x.deb ------------------------------ new debian package, version 2.0. size 202036 bytes: control archive=1048 bytes. 718 bytes, 18 lines control 453 bytes, 6 lines md5sums 161 bytes, 4 lines shlibs 70 bytes, 2 lines triggers Package: libapbs1 Source: apbs Version: 1.5+dfsg1-3 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 627 Depends: libc6 (>= 2.29), libgomp1 (>= 4.9), libmaloc1 (>= 0.2-1) Section: libs Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the libapbs_* shared libraries. drwxr-xr-x root/root 0 2020-04-03 04:05 ./ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/ -rw-r--r-- root/root 206768 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_generic.so.1 -rw-r--r-- root/root 141232 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_mg.so.1 -rw-r--r-- root/root 194328 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_pmgc.so.1 -rw-r--r-- root/root 79792 2020-04-03 04:05 ./usr/lib/s390x-linux-gnu/libapbs_routines.so.1 drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/libapbs1/ -rw-r--r-- root/root 3527 2020-04-03 04:05 ./usr/share/doc/libapbs1/changelog.Debian.gz -rw-r--r-- root/root 3720 2020-04-03 04:05 ./usr/share/doc/libapbs1/copyright python3-apbslib_1.5+dfsg1-3_s390x.deb ------------------------------------- new debian package, version 2.0. size 91244 bytes: control archive=1812 bytes. 853 bytes, 19 lines control 1924 bytes, 25 lines md5sums 255 bytes, 12 lines * postinst #!/bin/sh 404 bytes, 12 lines * prerm #!/bin/sh Package: python3-apbslib Source: apbs Version: 1.5+dfsg1-3 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 694 Depends: libapbs1 (= 1.5+dfsg1-3), python3 (<< 3.9), python3 (>= 3.8~), python3:any, libc6 (>= 2.4), libmaloc1 (>= 0.2-1), libpython3.8 (>= 3.8.2) Section: python Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package provides the apbslib module for Python3 enabling Python applications to access apbs. drwxr-xr-x root/root 0 2020-04-03 04:05 ./ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/python3/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/lib/python3/dist-packages/apbslib/ -rw-r--r-- root/root 23 2020-04-03 04:05 ./usr/lib/python3/dist-packages/apbslib/__init__.py -rw-r--r-- root/root 133840 2020-04-03 04:05 ./usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-38-s390x-linux-gnu.so -rw-r--r-- root/root 14632 2020-04-03 04:05 ./usr/lib/python3/dist-packages/apbslib/apbslib.py drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/apbs/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/apbs/tools/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/apbs/tools/python/ -rw-r--r-- root/root 20999 2016-10-17 21:05 ./usr/share/apbs/tools/python/Makefile -rw-r--r-- root/root 898 2016-10-17 21:05 ./usr/share/apbs/tools/python/Makefile.am -rw-r--r-- root/root 20457 2016-10-17 21:05 ./usr/share/apbs/tools/python/Makefile.in -rw-r--r-- root/root 1834 2016-10-17 21:05 ./usr/share/apbs/tools/python/README -rw-r--r-- root/root 6111 2016-10-17 21:05 ./usr/share/apbs/tools/python/apbs.in -rw-r--r-- root/root 260299 2016-10-17 21:05 ./usr/share/apbs/tools/python/apbslib.c -rw-r--r-- root/root 14874 2016-10-17 21:05 ./usr/share/apbs/tools/python/apbslib.i -rw-r--r-- root/root 11686 2016-10-17 21:05 ./usr/share/apbs/tools/python/apbslib_wrap.doc -rw-r--r-- root/root 66 2016-10-17 21:05 ./usr/share/apbs/tools/python/ion.pqr -rw-r--r-- root/root 14079 2020-04-03 04:05 ./usr/share/apbs/tools/python/main.py -rw-r--r-- root/root 17884 2020-04-03 04:05 ./usr/share/apbs/tools/python/noinput.py drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/apbs/tools/python/vgrid/ -rw-r--r-- root/root 15551 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/Makefile -rw-r--r-- root/root 845 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/Makefile.am -rw-r--r-- root/root 15036 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/Makefile.in -rw-r--r-- root/root 1638 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/README -rw-r--r-- root/root 2980 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/average.py -rw-r--r-- root/root 14037 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/mergedx.py -rw-r--r-- root/root 2255 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/read.py -rw-r--r-- root/root 3038 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/vgrid.i -rw-r--r-- root/root 4449 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/vgrid.py -rw-r--r-- root/root 97218 2016-10-17 21:05 ./usr/share/apbs/tools/python/vgrid/vgridlib.c drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-03 04:05 ./usr/share/doc/python3-apbslib/ lrwxrwxrwx root/root 0 2020-04-03 04:05 ./usr/share/doc/python3-apbslib/changelog.Debian.gz -> ../libapbs1/changelog.Debian.gz -rw-r--r-- root/root 3720 2020-04-03 04:05 ./usr/share/doc/python3-apbslib/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 2459696 Build-Time: 857 Distribution: groovy-proposed Host Architecture: s390x Install-Time: 15 Job: apbs_1.5+dfsg1-3.dsc Machine Architecture: s390x Package: apbs Package-Time: 874 Source-Version: 1.5+dfsg1-3 Space: 2459696 Status: successful Version: 1.5+dfsg1-3 -------------------------------------------------------------------------------- Finished at 20200508-0446 Build needed 00:14:34, 2459696k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19276035 Scanning for processes to kill in build PACKAGEBUILD-19276035