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Fixed APBS directory structure

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This commit is contained in:
Nathan Baker
2014-01-02 12:15:02 -08:00
parent c86065cd47
commit 55301efbe4
1076 changed files with 575770 additions and 0 deletions
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649
CMakeLists.txt Normal file
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cmake_minimum_required (VERSION 2.8)
################################################################################
# TODO: Add licensing and authorship information
# TODO: Test with FEtk build
# TODO: Handle special mac dependencies
# (configure.ac:1306)
################################################################################
################################################################################
# Future Enchancements
# --------------------
# [ ] Adding a profiling mode set by a flag
# [ ] Add functionality for creating rpm and deb packages
################################################################################
################################################################################
# Test platforms
# --------------
# [x] Ubuntu x86_64
# [x] Ubuntu i386
# [ ] Redhat 5
# [x] Redhat 6
# [x] Mac OSX
# [ ] Windows 7 x86_64
# [ ] Windows 7 i386
# [x] Windows 7 with Cygwin
# [ ] Windows 7 with Mingw
################################################################################
################################################################################
# Set up basic project stuff #
################################################################################
include(CheckIncludeFiles)
include(CheckFunctionExists)
include(ExternalProject)
set(APBS_VERSION "1.4")
set(PACKAGE_STRING ${APBS_VERSION})
set(CMAKE_BUILD_TYPE "RELWITHDEBINFO")
project(apbs)
OPTION (BUILD_SHARED_LIBS "Build shared libraries." OFF)
################################################################################
# Set project paths #
################################################################################
message(STATUS "Setting project paths")
set(CMAKE_C_FLAGS -std=c99)
set(APBS_ROOT ${PROJECT_SOURCE_DIR})
set(EXECUTABLE_OUTPUT_PATH ${APBS_ROOT}/bin)
set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib)
set(TOOLS_PATH ${APBS_ROOT}/tools)
set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
set(LIBRARY_INSTALL_PATH lib)
set(HEADER_INSTALL_PATH include/apbs)
set(EXECUTABLE_INSTALL_PATH bin)
set(SHARE_INSTALL_PATH share/apbs)
find_file(CONTRIB_PATH "contrib" PATHS "${APBS_ROOT}"
DOC "The path to contributed modules for apbs"
)
set(SYS_LIBPATHS /usr/lib64)
#list(APPEND SYS_LIBPATHS /usr/lib64)
################################################################################
# Set up temporary files and directories #
################################################################################
file(MAKE_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}/temp)
################################################################################
# Set the lookup paths for external library dependencies #
################################################################################
message(STATUS "Setting lookup paths for headers and libraries")
set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
list(APPEND CMAKE_INCLUDE_PATH /usr/include)
list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow")
################################################################################
# Enable ansi pedantic compiling #
################################################################################
option(ENABLE_PEDANTIC "Enable the pedantic ansi compilation" OFF)
if(ENABLE_PEDANTIC)
ADD_DEFINITIONS("-Wall -pedantic -ansi")
message(STATUS "Pedantic compilation enabled")
endif()
################################################################################
# Determine Machine Epsilon values #
################################################################################
OPTION(CHECK_EPSILON "" YES)
if(CHECK_EPSILON)
message(STATUS "Computing machine epsilon values")
try_run(
FLOAT_EPSILON_COMPILED
FLOAT_EPSILON_COMPUTED
${EXECUTABLE_OUTPUT_PATH}/temp
${APBS_ROOT}/src/.config/float_epsilon.c
RUN_OUTPUT_VARIABLE FLOAT_EPSILON_OUTPUT
)
if(FLOAT_EPSILON_COMPUTED)
message(STATUS "Floating point epsilon is ${FLOAT_EPSILON_OUTPUT}")
set(FLOAT_EPSILON ${FLOAT_EPSILON_OUTPUT})
else()
message(FATAL_ERROR "Couldn't compute floating point machine epsilon")
endif()
try_run(
DOUBLE_EPSILON_COMPILED
DOUBLE_EPSILON_COMPUTED
${EXECUTABLE_OUTPUT_PATH}/temp
${APBS_ROOT}/src/.config/double_epsilon.c
RUN_OUTPUT_VARIABLE DOUBLE_EPSILON_OUTPUT
)
if(DOUBLE_EPSILON_COMPUTED)
message(STATUS "Double precision epsilon is ${DOUBLE_EPSILON_OUTPUT}")
set(DOUBLE_EPSILON ${DOUBLE_EPSILON_OUTPUT})
else()
message(FATAL_ERROR "Couldn't compute double precision machine epsilon")
endif()
else()
set(FLOAT_EPSILON "1.19209290e-7")
set(DOUBLE_EPSILON "2.2204460492503131e-16")
endif()
################################################################################
# Find some libraries #
################################################################################
if(NOT WIN32)
find_library(MATH_LIBRARY "m")
list(APPEND APBS_LIBS -lm)
endif()
################################################################################
# Check for a few required functions #
################################################################################
CHECK_FUNCTION_EXISTS(time HAVE_TIME_FUNC)
if(NOT HAVE_TIME_FUNC)
message(FATAL_ERROR "Required time function not found")
endif()
CHECK_FUNCTION_EXISTS(rand HAVE_RAND_FUNC)
if(NOT HAVE_RAND_FUNC)
message(FATAL_ERROR "Required rand function not found")
endif()
CHECK_FUNCTION_EXISTS(srand HAVE_SRAND_FUNC)
if(NOT HAVE_SRAND_FUNC)
message(FATAL_ERROR "Required srand function not found")
endif()
option(ENABLE_BEM "Boundary element method using TABIPB" ON)
if(ENABLE_BEM)
set(TABI tabipb)
set(TABI_PATH ${CONTRIB_PATH}/tabipb)
ExternalProject_add(
${TABI}
URL file://${TABI_PATH}
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${APBS_ROOT}
-DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
)
if(BUILD_SHARED_LIBS)
set(TABI_LIBRARY_BASENAME ${CMAKE_SHARED_LIBRARY_PREFIX}${TABI}${CMAKE_SHARED_LIBRARY_SUFFIX})
else()
set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX})
endif()
install(
FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod
DESTINATION ${LIBRARY_INSTALL_PATH}
)
set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME})
set(LIBGFORTRAN_NAME ${CMAKE_SHARED_LIBRARY_PREFIX}gfortran${CMAKE_SHARED_LIBRARY_SUFFIX})
execute_process(COMMAND gfortran --print-file-name ${LIBGFORTRAN_NAME}
OUTPUT_VARIABLE LIBGFORTRANPATH
RESULT_VARIABLE HAVE_GFORTRAN
)
if(HAVE_GFORTRAN GREATER 0)
message(FATAL_ERROR gfortran is currently required for using BEM/TABIPB in APBS)
endif()
get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH)
find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH})
list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" )
endif()
find_file( # this should be find path...
FETK_PATH
NAMES fetk
PATHS ${SYS_LIBPATHS} /data/work/source . ..
DOC "Use an external fetk library")
if(FETK_PATH)
include_directories(${FETK_PATH}/include)
message(STATUS "Found fetk: ${FETK_PATH}")
else()
message(WARNING "Did not find fetk")
endif()
find_library(MALOC_LIBRARY "maloc"
PATHS ${FETK_PATH}/lib ${CONTRIB_PATH}
DOC "The fetk/maloc library"
)
if(MALOC_LIBRARY)
message(STATUS "External maloc library was found: ${MALOC_LIBRARY}")
else()
message(WARNING "External maloc library was not found.")
endif()
if(MALOC_LIBRARY AND ENABLE_FETK)
include_directories(${FETK_PATH}/include/maloc)
SET(HAVE_MALOC_H YES)
else()
CHECK_INCLUDE_FILES(maloc/maloc.h HAVE_MALOC_H)
endif()
if(HAVE_MALOC_H)
message(STATUS "External maloc headers found")
else()
message(WARNING "External maloc headers not found.")
endif()
if(NOT (HAVE_MALOC_H AND MALOC_LIBRARY))
message(STATUS "Using internal contributed maloc library")
ExternalProject_add(
"maloc"
URL file://${CONTRIB_PATH}/maloc.tar.gz
SOURCE_DIR ${CONTRIB_PATH}/maloc
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${APBS_ROOT}
-DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
)
include_directories(${APBS_ROOT}/include)
if(BUILD_SHARED_LIBS)
set(MALOC_LIBRARY_BASENAME ${CMAKE_SHARED_LIBRARY_PREFIX}maloc${CMAKE_SHARED_LIBRARY_SUFFIX})
else()
set(MALOC_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}maloc${CMAKE_STATIC_LIBRARY_SUFFIX})
endif()
install(
FILES ${LIBRARY_OUTPUT_PATH}/${MALOC_LIBRARY_BASENAME}
DESTINATION ${LIBRARY_INSTALL_PATH}
)
set(MALOC_LIBRARY ${LIBRARY_OUTPUT_PATH}/${MALOC_LIBRARY_BASENAME})
endif()
list(APPEND APBS_LIBS -lmaloc)
################################################################################
# Handle the finite element solver dependencies #
################################################################################
option(ENABLE_FETK "Enable the finite element solver" OFF)
if(ENABLE_FETK)
message(STATUS "Checking for fetk components")
set(FETK_ENALBED 1)
list(APPEND APBS_LIBS "-lstdc++")
list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack
-lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline )
SET(HAVE_MC_H YES)
endif()
################################################################################
# Handle conditional fast mode #
################################################################################
option(ENABLE_FAST "Enable fast mode" OFF)
if(ENABLE_FAST)
set(APBS_FAST 1)
message(STATUS "Fast mode enabled")
endif()
################################################################################
# Handle conditional TINKER support #
################################################################################
option(ENABLE_TINKER "Enable TINKER support" OFF)
if(ENABLE_TINKER)
set(WITH_TINKER 1)
message(STATUS "Tinker enabled")
endif()
################################################################################
# Handle conditional availability of macro embedding #
################################################################################
try_compile(
HAVE_EMBED
${APBS_ROOT}/build
${APBS_ROOT}/src/.config/embed_test.c
)
# TODO: Determine if the EMBED macro is even used
################################################################################
# Handle conditional debug building #
################################################################################
option(ENABLE_DEBUG "Enable debugging mode" OFF)
if(ENABLE_DEBUG)
set(CMAKE_BUILD_TYPE Debug)
set(DEBUG 1)
message(STATUS "Debugging compilation enabled")
endif()
################################################################################
# Enable inline functions conditionally dependant on debug mode #
################################################################################
option(ENABLE_INLINE "Enable inline functions" ON)
if(ENABLE_INLINE)
set(APBS_NOINLINE 1)
message(STATUS "Inline functions enabled")
endif()
################################################################################
# Handle conditional building with quiet mode #
################################################################################
option(ENABLE_QUIET "Enable quiet mode" OFF)
if(ENABLE_QUIET)
set(VAPBSQUIET 1)
message(STATUS "Quiet mode enabled")
endif()
################################################################################
# Handle conditional building with verbose debugging information printouts #
################################################################################
option(ENABLE_VERBOSE_DEBUG "Enable verbose debugging mode" OFF)
if(ENABLE_VERBOSE_DEBUG)
set(VERBOSE_DEBUG 1)
message(STATUS "Verbose debugging mode enabled")
endif()
################################################################################
# Configure Python Wrappers #
################################################################################
option(ENABLE_PYTHON "Enable python wrappers" OFF)
option(MAX_MEMORY "Set the maximum memory (in MB) to be used for a job" OFF)
if(ENABLE_PYTHON)
message(STATUS "Looking for python components")
if(NOT CMAKE_COMPILER_IS_GNUCC)
message(FATAL_ERROR "Python wrappers require GNU compilers")
endif()
find_package(PythonInterp)
if(NOT PYTHON_EXECUTABLE)
message(FATAL_ERROR "Couldn't find python interpreter")
endif()
find_package(PythonLibs)
if(NOT PYTHON_LIBRARY)
message(FATAL_ERROR "Couldn't find python libraries")
endif()
# TODO: Handle special flags for Python linking on different platforms
# TODO: Handle special flags for Python linking with intel compiler
# ${PYTHON_LFLAGS} perhaps?
set(MODULE_PROBE_PY "")
list(APPEND MODULE_PROBE_PY "from sys import stdout")
list(APPEND MODULE_PROBE_PY "from distutils.sysconfig import get_python_lib")
list(APPEND MODULE_PROBE_PY "stdout.write( get_python_lib() )")
execute_process(
COMMAND ${PYTHON_EXECUTABLE} -c "${MODULE_PROBE_PY}"
ERROR_QUIET
OUTPUT_VARIABLE PYTHON_MODULES
)
if(NOT PYTHON_MODULES)
message(FATAL_ERROR "Coudln't determine location of python modules")
endif()
if(NOT MAX_MEMORY)
set(MAX_MEMORY "-1")
endif()
# TODO: these can't e right...
set(SERVICEURL "http://kryptonite.nbcr.net/opal2/services/apbs_1.3")
set(PARALLELSERVICEURL "http://oolite.calit2.optiputer.net/opal2/services/apbs-parallel-1.3")
configure_file(
${APBS_ROOT}/src/.config/ApbsClient.py.in
${EXECUTABLE_OUTPUT_PATH}/ApbsClient.py
)
endif()
################################################################################
# Handle conditional building with OpenMP #
################################################################################
option(ENABLE_OPENMP "Enable OpenMP parallelism" ON)
if(ENABLE_OPENMP)
if(NOT ENABLE_DEBUG)
message(STATUS "Checking for OpenMP")
find_package(OpenMP)
if(OPENMP_FOUND)
message(STATUS "OpenMP support enabled")
add_definitions("${OpenMP_C_FLAGS}")
list(APPEND APBS_LIBS ${OpenMP_C_FLAGS})
else()
message(WARNING "OpenMP was not found. OpenMP support disabled")
endif()
else()
message(WARNING "OpenMP may not be enabled in debugging mode")
endif()
endif()
################################################################################
# Handle conditional building with MPI Support #
################################################################################
option(ENABLE_MPI "Enable MPI parallelism" OFF)
if(ENABLE_MPI)
if(NOT ENABLE_DEBUG)
message(STATUS "Checking for MPI")
find_package(MPI)
if(MPI_FOUND)
message(STATUS "MPI support enabled")
include_directories(${MPI_INCLUDE_PATH})
list(APPEND APBS_LIBS ${MPI_LIBRARIES})
else()
message(WARNING "MPI was not found; disabling")
endif()
else()
message(WARNING "MPI may not be enabled in debugging mode")
endif()
endif()
################################################################################
# Handle library checks for embedded unix environments in windows #
################################################################################
if(MINGW)
message(STATUS "Checking for wsock32 in MinGW environment")
find_library(
MINGW_WSOCK32
NAMES wsock32
PATHS ${SYS_LIBPATHS}
DOC "The wsock32 library"
)
if(MINGW_WSOCK32)
message(STATUS "The wsock32 library was found: ${MINGW_HAS_WSOCK32}")
else()
message(FATAL_ERROR "The wsock32 library was not fond")
endif()
endif()
if(CYGWIN)
message(STATUS "Checking for wsock32 in Cygwin environment")
find_library(
CYGWIN_WSOCK32
NAMES wsock32
PATHS ${SYS_LIBPATHS}
DOC "The wsock32 library"
)
if(CYGWIN_WSOCK32)
message(STATUS "The wsock32 library was found: ${CYGWIN_WSOCK32}")
list(APPEND APBS_LIBS ${CYGWIN_WSOCK32})
else()
message(FATAL_ERROR "The wsock32 library was not fond")
endif()
set(HAVE_CYGWIN 1)
endif()
if(NOT CYGWIN AND NOT MINGW AND WIN32)
list(APPEND APBS_LIBS wsock32)
ADD_DEFINITIONS("/D _CRT_SECURE_NO_WARNINGS")
endif()
message("libs: " ${APBS_LIBS})
################################################################################
# Build APBS sources #
################################################################################
include_directories(${APBS_ROOT}/src)
add_subdirectory(src)
################################################################################
# Build APBS documentation #
################################################################################
option(BUILD_DOC "Build/Rebuild documentation using doxygen" OFF)
if(BUILD_DOC)
message(STATUS "Building documentation enabled")
add_subdirectory(doc)
endif()
################################################################################
# Handle conditional building with verbose debugging information printouts #
################################################################################
option(BUILD_TOOLS "Build supplemental tools" ON)
if(BUILD_TOOLS)
message(STATUS "Supplemental tools enabled")
add_subdirectory(tools)
endif()
################################################################################
# Set up additional directories to install #
################################################################################
install(
DIRECTORY ${APBS_ROOT}/doc
DESTINATION ${SHARE_INSTALL_PATH}
)
install(
DIRECTORY ${APBS_ROOT}/examples
DESTINATION ${SHARE_INSTALL_PATH}
)
install(
DIRECTORY ${APBS_ROOT}/tests
DESTINATION ${SHARE_INSTALL_PATH}
FILES_MATCHING
PATTERN "*.py"
PATTERN "README"
)
install(
DIRECTORY ${APBS_ROOT}/tools
DESTINATION ${SHARE_INSTALL_PATH}
PATTERN "CMakeLists.txt" EXCLUDE
)
if(NOT HAVE_MALOC_H)
message(STATUS "Installing maloc headers")
install(
DIRECTORY ${APBS_ROOT}/include/maloc
DESTINATION ${HEADER_INSTALL_PATH}/..
)
endif()
################################################################################
# Optionally build iAPBS interface #
################################################################################
option(ENABLE_iAPBS "Enable iAPBS" OFF)
if(ENABLE_iAPBS)
message(STATUS "Building of iAPBS interface enabled")
add_subdirectory(contrib/iapbs/src)
list(APPEND APBS_LIBS ${iAPBS_LIBRARY})
endif()
################################################################################
# Clean up temporary files and directories #
################################################################################
file(REMOVE_RECURSE ${EXECUTABLE_OUTPUT_PATH}/temp)

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#!/bin/bash
rm -rf ../bin/* ../tools/bin/* ../lib/* CMakeFiles CMakeCache.txt cmake_install.cmake Makefile src install_manifest.txt apbs.cbp maloc-prefix tools fontconfig ../tests/*.pyc ../tests/io.mc ../tests/test.log doc ../doc/programmer/html ../doc/programmer/programmer.html ../doc/programmer/mainpage.h ../doc/programmer/Doxyfile ../doc/programmer/latex ../doc/programmer/programmer.pdf
find .. -name '*~' | xargs rm

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buildWithFETK.sh Executable file
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#!/bin/bash
#run this in apbsroot to build apbs with fetk support
#download, hack (maloc incompatability), and build fetk
wget http://www.fetk.org/codes/download/fetk-1.5.tar.gz
tar xzvf fetk-1.5.tar.gz
cd fetk
echo 'VPUBLIC int Vio_getc(Vio *thee){ ASC *asc; asc = thee->axdr; return asc->buf[asc->pos++]; }' >> maloc/src/vsys/vio.c
echo | ./fetk-build maloc punc gamer mc
cp -r build/x86_64-unknown-linux-gnu/include/ .
cp -r build/x86_64-unknown-linux-gnu/lib/ .
#uncomment for static library support
#cd lib
#rename .la .a *
#cd ..
#build apbs
cd ../build
cmake -DENABLE_FETK=YES -DBUILD_SHARED_LIBS=YES ..
make
#test fem support
cd ../examples/born
../../bin/apbs apbs-mol-fem.in
../../bin/apbs apbs-smol-fem.in
#../../bin/apbs apbs-mol-fem-extmesh.in

0
contrib/iapbs/AUTHORS Normal file
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39
contrib/iapbs/CMakeLists.txt Normal file
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################################################################################
# Set up basic project stuff #
################################################################################
cmake_minimum_required(VERSION 2.6)
include(CheckIncludeFiles)
include(CheckFunctionExists)
include(CheckSymbolExists)
include(CheckTypeSize)
include(ExternalProject)
set(iAPBS_VERSION "3.0.0")
#set(PACKAGE_STRING ${iAPBS_VERSION})
PROJECT(iAPBS)
#PROJECT(iAPBS C Fortran)
#ENABLE_LANGUAGE(Fortran)
################################################################################
# Set project paths #
################################################################################
message(STATUS "Setting iAPBS project paths")
set(iAPBS_ROOT ${PROJECT_SOURCE_DIR})
set(EXECUTABLE_OUTPUT_PATH ${iAPBS_ROOT}/bin)
set(LIBRARY_OUTPUT_PATH ${iAPBS_ROOT}/lib)
set(LIBRARY_INSTALL_DIR lib)
################################################################################
# add src
################################################################################
add_subdirectory(src)
#get_cmake_property(_variableNames VARIABLES)
#foreach (_variableName ${_variableNames})
# message(STATUS "${_variableName}=${${_variableName}}")
#endforeach()

340
contrib/iapbs/COPYING Normal file
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GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Library General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
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you have. You must make sure that they, too, receive or can get the
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We protect your rights with two steps: (1) copyright the software, and
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The precise terms and conditions for copying, distribution and
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Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.

145
contrib/iapbs/ChangeLog Normal file
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@@ -0,0 +1,145 @@
#######################################################################
#
#
# iAPBS Release 3.2.0 ChangleLog
#
#
#######################################################################
----------------------------------------------------------------------
Release 3.2.0 September 3, 2013
- Fixed a bug in modules/Amber/amber.f90 (reported by Marek Maly)
----------------------------------------------------------------------
Release 3.1.0 March 15, 2013
- The NAMD module has been updated to work with NAMD version 2.9.
- Several small bug fixes in the CHARMM module.
----------------------------------------------------------------------
Release 3.0.0 February 7, 2013
- The API has been extended, support for grid data writing and reading
on the fly added.
- New application module for Rosetta, thanks to Sachko Honda. This
module is distributed with Rosetta.
----------------------------------------------------------------------
Release 2.3.0, December 6, 2012
- Converted to use cmake
- Tighter integration with APBS build process. Now builds with
"cmake -DENABLE_iAPBS=ON .."
----------------------------------------------------------------------
Release 2.2.0, October 10, 2012
- Updated to work with the latest APBS git code
----------------------------------------------------------------------
Release 2.1.0, January 11, 2012
- Updated Amber, NAMD and CHARMM modules.
- Fixed a couple of low priority bugs.
----------------------------------------------------------------------
Release 2.0.0, December 8, 2011
- iAPBS is included in APBS
- Updated apolar section of the code.
- Cleaned tests.
----------------------------------------------------------------------
Release 1.2.0, March 15, 2011
- Support for NAMD pre-2.8.
- Hooks for zlib support.
----------------------------------------------------------------------
Release 1.1.0, February 28, 2011
- Updated for APBS 1.3
- Added a feature for writing numbered elstat potential files during
an MD in Amber
- Updated CHARMM module, docs and test cases
----------------------------------------------------------------------
Release 1.0.0, November 18, 2009
- Updated the NAMD module for NAMD version 2.7b2 and the current CVS
tree.
- Updated the Amber module to work with Amber11 CVS tree.
----------------------------------------------------------------------
Release 0.8.0, April 30, 2009
- Updated the NAMD module and associated files for NAMD version 2.7b1
and newer. Extended the NAMD module functionality for writing and
reading APBS maps. This is a release candidate for an official NAMD
module release.
----------------------------------------------------------------------
Release 0.7.0, April 7, 2009
- Added patch for CHARMM c35b2
----------------------------------------------------------------------
Release 0.6.0, Jan 14, 2009
- Added support for diel and kappa map reading/writing.
- Added support for charge map reading.
- CHARMM and Amber modules updated for the new functionality.
----------------------------------------------------------------------
Release 0.5.0, Oct 14, 2008
- Added rudimentary MPI support
----------------------------------------------------------------------
Release 0.4.0, Sep 22, 2008
- A fix for APBS memory leak for multiple iAPBS calls.
----------------------------------------------------------------------
Release 0.3.0, May 28, 2008
- Updated the interface to match APBS version 1.0.0
- Added basic NAMD module support.
----------------------------------------------------------------------
Release 0.2.0, June 21, 2006
- Updated the interface to match APBS version 0.4.0.
- Amber module available together with docs and examples.
- Manual installation converted to autotools.
- Added support for linking with C++ applications (thanks to Gernot
Kieseritzky).
----------------------------------------------------------------------
Release 0.1.0 May 25, 2005
- Initial public release.
- CHARMM module available with docs and examples.

3
contrib/iapbs/INSTALL Normal file
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@@ -0,0 +1,3 @@
see doc/index.html for installation instructions

0
contrib/iapbs/NEWS Normal file
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2
contrib/iapbs/README Normal file
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@@ -0,0 +1,2 @@
Please see doc/index.html for the documentation and
doc/license/LICENSE.txt or COPYING for license information.

10
contrib/iapbs/etc/iapbs-version.mk Normal file
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@@ -0,0 +1,10 @@
#
# $Id: iapbs-version.mk,v 1.4 2007/09/26 00:28:39 rok Exp $
#
VERSION.MAJOR = 2
VERSION.MINOR = 3
VERSION.PATCHLEVEL = 0
VERSION = $(VERSION.MAJOR).$(VERSION.MINOR).$(VERSION.PATCHLEVEL)
IAPBS_VERSION = $(VERSION)

1250
contrib/iapbs/modules/Amber/apbs.f90 Normal file
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File diff suppressed because it is too large Load Diff

219
contrib/iapbs/modules/Amber/apbs_vars.f90 Normal file
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@@ -0,0 +1,219 @@
! $Id: apbs_vars.f90 549 2011-12-08 21:21:18Z rok $
!
#include "../include/dprec.fh"
MODULE apbs_vars
#ifdef APBS
use file_io_dat, only : MAX_FN_LEN
!-----------------------------------------------------------------------
!
! iAPBS variables definition
!
! Similar type of varibles are packed together (integer/integer and
! real/real) to mimize fortran/C passing incompatabilities.
!
! For detailed description of individual variables please see
! the iAPBS Programmer's Guide.
!
!-----------------------------------------------------------------------
! max number of counterions
INTEGER, PARAMETER :: MAXION = 10
! static dimensions (for now) rokFIXME
INTEGER, PARAMETER :: APBSNATOMS = 10000
!-----------------------------------------------------------------------
! int ispara; : 1 => is a parallel calculation,
! 0 => is not
INTEGER :: ispara
!-----------------------------------------------------------------------
! r_param memebers
! 1 double pdie; : Solute dielectric
! 2 double sdie; : Solvent dielectric
! 3 double srad; : Solvent radius
! 4 double swin; : Cubic spline window
! 5 double temp; : Temperature (in K)
! 6 double sdens; : Vacc sphere density
! 7 double gamma; : Surface tension for apolar energies/forces
! (in kJ/mol/A^2)
! 8 double smvolume
! 9 double smsize
!
_REAL_ :: r_param(9)
!-----------------------------------------------------------------------
! i_param members
!
! 1 int type; : What type of MG calculation?
! 0: sequential manual
! 1: sequential auto-focus
! 2: parallel auto-focus
! 2 int nlev; : Levels in multigrid hierarchy
! 3 int cmeth; : Centering method:
! 0: center on point,
! 1: center on molecule
! 4 int ccmeth; : Coarse grid centering method: 0 => center
! on point, 1 => center on molecule
! 5 int fcmeth; : Fine grid centering method: 0 => center on
! point, 1 => center on molecule
! 6 int chgm Types of charge discretization methods
! 0: Trilinear interpolation of charge to
! 8 nearest grid points. The traditional method;
! not particularly good to use with PBE forces.
! 1: Cubic B-spline across nearest- and
! next-nearest-neighbors. Mainly for use in
! grid-sensitive applications
! (such as force calculations).
!
! 7 int nonlin; : 0 => LPBE, 1 => NPBE, 2: LRPBE,
! 3: NRPBE, 4: SMPBE
! 8 int bcfl; : Boundary condition: 0 => zero, 1 => single
! Debye-Huckel sphere, 2 => multiple Debye-
! Huckel spheres, 4 => focusing
! 9 int srfm; : Surface calculation method
! 0: Mol surface for epsilon; inflated VdW
! for kappa; no smoothing
! 1: As 0 with harmoic average
! smoothing
! 2: Cubic spline
!10 int calcenergy; : Energy calculation
! 0: don't calculate out energy
! 1: calculate total energy
! 2: calculate total energy and all energy
! components
!11 int calcforce; : Atomic forces I/O
! 0: don't calculate forces
! 1: calculate net forces on molecule
! 2: calculate atom-level forces
!12 int wpot : write potential map
!13 int wchg : write charge map
!14 int wsmol : write smol map
!15 int wkappa : write kappa map
!16 int wdiel : write diel maps (x, y and z)
!17 int watompot : write atom potentials map
!18 int rpot : read pot map
!19 dummy
!20 calcnpforce
!21 calcnpenergy
!22 int nion; : Number of counterion species
!23 int rchg; : read charge map
!24 int rkappa : read kappa map
!25 int rdiel : read diel maps (x, y and z)
INTEGER :: i_param(25)
!-----------------------------------------------------------------------
! int dime[3]; : Grid dimensions
! int pdime[3]; : Grid of processors to be used in
! calculation
!
INTEGER :: dime(3), pdime(3)
!-----------------------------------------------------------------------
! double grid[3]; : Grid spacings
! double glen[3]; : Grid side lengths.
! double center[3]; : Grid center. If ispart = 0, then this is
! only meaningful if cmeth = 0. However, if
! ispart = 1 and cmeth = 0, then this is the
! center of the non-disjoint (overlapping)
! partition. If ispart = 1 and cmeth = 1, then
! this is the vector that must be added to the
! center of the molecule to give the center of
! the non-disjoint partition.
! double cglen[3]; : Coarse grid side lengths
! double fglen[3]; : Fine grid side lengths
! double ccenter[3]; : Coarse grid center.
! double fcenter[3]; : Fine grid center.
! double ofrac; : Overlap fraction between procs
!
_REAL_ :: grid(3), glen(3), center(3), cglen(3), fglen(3)
_REAL_ :: ccenter(3), fcenter(3), ofrac
!-----------------------------------------------------------------------
! mobile ion definition
!
! double ionq[MAXION]; : Counterion charges (in e)
! double ionc[MAXION]; : Counterion concentrations (in M)
! double ionr[MAXION]; : Counterion radii (in A)
!
_REAL_ :: ionq(MAXION), ionc(MAXION), ionrr(MAXION)
!-----------------------------------------------------------------------
! internal PB radii and charges
_REAL_ :: pbradii(APBSNATOMS) ! PB radii
_REAL_ :: pbcg(APBSNATOMS) ! PB charges
!-----------------------------------------------------------------------
! solvation energy and forces saved for use later
_REAL_ :: senelec, sennp
_REAL_ :: solvfrcx(APBSNATOMS)
_REAL_ :: solvfrcy(APBSNATOMS)
_REAL_ :: solvfrcz(APBSNATOMS)
_REAL_ :: geom_upd_limit, evdw_upd_limit, saveevdw
_REAL_ :: savedx(APBSNATOMS)
_REAL_ :: savedy(APBSNATOMS)
_REAL_ :: savedz(APBSNATOMS)
!-----------------------------------------------------------------------
! some integer variables
!
! napbs - how often we calculate APBS forces during MD/minimization
! umeth - forces update method
! apbs_debug - debug/verbosity value [0-5]
! apbs_print - debug/verbosity value [0-5]
! radiopt - optimization of radii method (see the source for details)
!
INTEGER :: napbs, umeth, apbs_debug, apbs_print, radiopt
!-----------------------------------------------------------------------
! logical variables
!
! qapbs: were all parameters parsed?
! qfapbs: do we want to calculate solvation forces?
! qaparsed: did we parse all user options?
! dime_updates: update grid dimensions on the fly
LOGICAL :: qapbs, qfapbs, qaparsed, dime_updates
!-----------------------------------------------------------------------
! string variables
!
! pqr: file name for an external pqr file (reading radii and charges)
!
CHARACTER(len=MAX_FN_LEN) pqr
!-----------------------------------------------------------------------
!
! commons
!
!-----------------------------------------------------------------------
!
! disable COMMONs, we are using modules
!
!-----------------------------------------------------------------------
! integer common
! COMMON / apbs_int / ispara, i_pbeparm, set_pbeparm, i_mgparm, &
! dime, pdime, set_mgparm, napbs, umeth, apbs_debug
!-----------------------------------------------------------------------
! double precision common
! COMMON / apbs_real / r_pbeparm, ionq, ionc, ionrr, &
! grid, glen, center, cglen, fglen, &
! ccenter, fcenter, ofrac, pbcg, pbradii, &
! senelec, sennp, solvfrcx, solvfrcy, solvfrcz
!-----------------------------------------------------------------------
! logical common
! COMMON / apbs_logical/ qapbs, qfapbs, qaparsed
!
!
! SAVE / apbs_int /
! SAVE / apbs_real /
! SAVE / apbs_logical /
#endif /* APBS */
END MODULE apbs_vars

19
contrib/iapbs/modules/Amber/examples/md.in Normal file
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@@ -0,0 +1,19 @@
Example of APBS implicit solvent dynamics
&cntrl
ntx=1, irest=0, imin=0,
ntpr=10, ntwx=500, nscm=100, ntwr=5000,
dt=0.001, nstlim=50,
temp0=300, tempi=0, ntt=1, tautp=0.1,
igb=6, cut=12.0, ntb=0,
ntc=2, ntf=2, tol=0.000001
/
&apbs
apbs_print=0,
dime = 33, 33, 33,
cglen = 10.0, 10.0, 10.0,
fglen = 9.0, 9.0, 9.0,
nion=2,
ionq = 1.0, -1.0,
ionc = 0.15, 0.15,
ionrr = 2.0, 2.0,
&end

17
contrib/iapbs/modules/Amber/examples/solvation.in Normal file
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@@ -0,0 +1,17 @@
APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_print=1
dime = 33, 33, 33
cglen = 10.0, 10.0, 10.0
fglen = 8.0, 8.0, 8.0
nion=2,
ionq = 1.0, -1.0,
ionc = 0.15, 0.15,
ionrr = 2.0, 2.0,
&end

16
contrib/iapbs/modules/Amber/examples/vis.in Normal file
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@@ -0,0 +1,16 @@
APBS visualization example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0
ntpr=1,
/
&apbs
apbs_print=1,
calc_type = 0,
grid = 0.5, 0.5, 0.5,
srad = 0.7,
wpot = 1, wchg = 1, wsmol =1,
sp_apbs=.true.,
&end

294
contrib/iapbs/modules/Amber/patches/amber10_mm_pbsa.patch Normal file
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@@ -0,0 +1,294 @@
diff -ur mm_pbsa.orig/mm_pbsa_calceneent.pm mm_pbsa/mm_pbsa_calceneent.pm
--- mm_pbsa.orig/mm_pbsa_calceneent.pm 2006-05-01 02:38:51.000000000 -0700
+++ mm_pbsa/mm_pbsa_calceneent.pm 2007-10-09 13:29:15.000000000 -0700
@@ -59,8 +59,9 @@
print OUT "MM\n" if($r_gen->{"MM"});
print OUT "GB\n" if($r_gen->{"GB"});
print OUT "PB\n" if($r_gen->{"PB"});
- print OUT "MS\n" if($r_gen->{"GB"} || $r_gen->{"PB"} || $r_gen->{"MS"}); # Implicit use of sander/pbsa SAS
- print OUT "NM\n" if($r_gen->{"NM"}); # calc if not MS set
+ print OUT "MS\n" if($r_gen->{"GB"} || ($r_gen->{"PB"} && ($r_del->{"PROC"} != 3)) ||
+ $r_gen->{"MS"}); # Implicit use of sander/pbsa SAS (disabled for iAPBS)
+ print OUT "NM\n" if($r_gen->{"NM"}); # calc if not MS set
}
else{
# Re-open existing file
@@ -138,6 +139,11 @@
my $pbsaout = "pbsa" . $suf . "." . $number . ".out";
&calc_pbsa(*OUT,"pbsa.in",$pbsaout,$ncrdfile,$npar,$r_gen,$r_pro,$r_del);
}
+ elsif($r_del->{"PROC"} == 3){
+ my $pbsaout = "iapbs" . $suf . "." . $number . ".out";
+ #my $pbsain = "iapbs" . $suf . ".in";
+ &calc_iapbs(*OUT,"iapbs.in",$pbsaout,$ncrdfile,$npar,$r_gen,$r_pro,$suf);
+ }
}
# Calc MS
@@ -288,6 +294,68 @@
unlink $pbsaout if( ! $r_gen->{"VERBOSE"});
}
+sub calc_iapbs(){
+################
+
+ # Parameters: $OUT, $pbsain, $pbsaout, $ncrdfile, $npar, $r_gen, $r_pro
+
+ my $OUT = shift;
+ my $pbsain = shift;
+ my $pbsaout = shift;
+ my $ncrdfile = shift;
+ my $npar = shift;
+ my $r_gen = shift;
+ my $r_pro = shift;
+ my $suf = shift;
+
+ print " Calc Amber/iAPBS\n";
+
+ my $command = $r_pro->{"IAPBS"} . " -O" .
+ " -i " . $pbsain .
+ " -o " . $pbsaout .
+ " -c " . $ncrdfile .
+ " -p " . $npar;
+
+
+ my $pqrfname = "";
+ $pqrfname = "com.pqr" if ($suf eq "_com");
+ $pqrfname = "rec.pqr" if ($suf eq "_rec");
+ $pqrfname = "lig.pqr" if ($suf eq "_lig");
+
+ my $lncommand = "ln -s " . $pqrfname . " ./pqr";
+ system($lncommand) && die ("Linking pqr file $pqrfname failed!\n");
+ system($command) && die(" $command not successful\n");
+ system("rm -f ./pqr");
+
+ # Write MM results
+ open(IN,"$pbsaout") || die(" $pbsaout not opened\n");
+ my $finalflg = 0;
+ my $line;
+ while(defined($line = <IN>)){
+ if($line =~ /FINAL RESULTS/){
+ $finalflg = 1;
+ }
+ elsif($finalflg > 0){
+ if ($line =~ /VDWAALS.+EEL.+EPB. += +(-?\d+\.\d+)/){
+ #print OUT $line;
+ # Convert to kT, because back-conversion to kcal/mol is done in
+ # mm_pbsa_statistics, subroutine treat_special
+ # (to be compatible with delphi calculation)
+ my $kcal2kt = 1000.0 * 4.184 / (300.0 * 8.314);
+ my $rfe = $1 * $kcal2kt;
+ printf OUT "%s %15.6f\n", "corrected reaction field energy:", $rfe;
+ }
+ elsif($line =~ /ENPOLAR +=/ && $r_gen->{"PB"} > 0 && $r_gen->{"MS"} == 0){
+ print OUT $line;
+ }
+ }
+ }
+ close(IN);
+
+ # Clean up MM
+ unlink $pbsaout;
+}
+
sub calc_delphi(){
##################
diff -ur mm_pbsa.orig/mm_pbsa_createinput.pm mm_pbsa/mm_pbsa_createinput.pm
--- mm_pbsa.orig/mm_pbsa_createinput.pm 2006-05-01 02:38:51.000000000 -0700
+++ mm_pbsa/mm_pbsa_createinput.pm 2007-10-09 13:25:20.000000000 -0700
@@ -51,6 +51,9 @@
elsif($r_del->{"PROC"} == 2){
&create_pbsa_input($r_gen, $r_san, $r_del);
}
+ elsif($r_del->{"PROC"} == 3){
+ &create_iapbs_input($r_gen, $r_san, $r_del);
+ }
}
if($r_gen->{"GC"} || $r_gen->{"AS"}){
@@ -372,7 +375,7 @@
close(OUT);
}
- }
+ }
return;
}
@@ -466,6 +469,83 @@
return;
}
+sub create_iapbs_input() {
+#########################
+ # Parameters: \%GEN,\%SAN,\%DEL
+ my $r_gen = shift;
+ my $r_san = shift;
+ my $r_del = shift;
+
+ print " iAPBS input\n";
+
+ my ($igb, $dielc, $epsin, $epsout, $istrng, $radiopt, $sprob,
+ $space, $maxitn, $npopt, $cavity_surften, $cavity_offset,
+ $srad, $bcfl, $srfm, $chgm, $swin);
+ # Do iAPBS calculation
+ $igb = 6;
+ $dielc = $r_san->{"DIELC"};
+ $epsin = $r_del->{"INDI"};
+ $epsout = $r_del->{"EXDI"};
+ my $pbions = "";
+ if(exists $r_del->{"ISTRNG"} && $r_del->{"ISTRNG"} > 0.0){
+ my $ionc = $r_del->{"ISTRNG"};
+ $pbions = " nion = 2, \n";
+ $pbions .= " ionq = 1.0, -1.0,\n";
+ $pbions .= " ionrr = 2.0, 2.0,\n";
+ $pbions .= " ionc = $ionc, $ionc,\n";
+ } else {
+ $pbions = " nion = 0,\n";
+ }
+ $radiopt = $r_del->{"RADIOPT"};
+ $sprob = $r_del->{"PRBRAD"};
+ $space = 1.0 / $r_del->{"SCALE"}->[0];
+ $srad = $r_del->{"SRAD"};
+ $bcfl = $r_del->{"BCFL"};
+ $srfm = $r_del->{"SRFM"};
+ $chgm = $r_del->{"CHGM"};
+ $swin = $r_del->{"SWIN"};
+ # ($dimex, $dimey, $dimez) = split(/,/,$r_del->{"DIME"});
+ # ($fglenx, $fgleny, $fglenz) = split(/,/,$r_del->{"FGLEN"});
+ # ($cglenx, $cgleny, $cglenz) = split(/,/,$r_del->{"CGLEN"});
+
+ my $name = "iapbs.in";
+ open(OUT,">$name") || die(" $name not opened\n");
+ print OUT "File generated by mm_pbsa.pl. Using iAPBS\n";
+ print OUT " &cntrl\n";
+ print OUT " ntf = 1, ntb = 0,\n";
+ print OUT " igb = ${igb}, dielc = ${dielc},\n";
+ print OUT " cut = 999.0, nsnb = 99999,\n";
+ print OUT " scnb = 2.0, scee = 1.2,\n";
+ print OUT " imin = 1, maxcyc = 0, ntmin = 2,\n";
+ print OUT " &end\n";
+ # Here, only REFE == 0 calculations are allowed, whereby the reference state
+ # is assumed to be INDI/INDI.
+ # Hence, only one pbsa calc with EXDI/INDI is performed,
+ # and the result taken is the reaction field energy
+ # (given as "ELE" in the pbsa output).
+ # Consider scaling of coulombic interactions as well (by DIELC) if using INDI != 1.
+ # If SALT > 0.0, only one calculation is done here (compared to delphi).
+ # For NLPB, see work of Tsui & Case, J. Phys. Chem. B 2001, 105, 11314
+ # and salt_contrib and process_phi scripts in delphi directory.
+ # Here, a PBTEMP of 300K is used to compute the Boltzmann factor for the salt effect.
+ # If a different temperature is specified here, also correct the factor for
+ # kcal/mol -> kT conversion in the subroutine calc_pbsa.
+
+ print OUT " &apbs\n";
+ print OUT " apbs_print=0, apbs_debug=0, calc_type = 0,\n";
+ print OUT " grid = ${space}, ${space}, ${space},\n";
+ print OUT " radiopt = ${radiopt}, pqr='pqr', \n";
+ print OUT " sdie = ${epsout}, pdie = ${epsin}, srad=${srad}, \n";
+ print OUT " cmeth=1, bcfl=${bcfl}, srfm=${srfm}, chgm=${chgm},\n";
+ print OUT $pbions;
+ print OUT " swin=${swin}, calcforce=0, calcnpenergy=1 \n";
+ print OUT " &end\n";
+
+ close(OUT);
+ return;
+}
+
+
sub create_makecrd_input(){
###########################
diff -ur mm_pbsa.orig/mm_pbsa_readinput.pm mm_pbsa/mm_pbsa_readinput.pm
--- mm_pbsa.orig/mm_pbsa_readinput.pm 2006-05-01 02:38:51.000000000 -0700
+++ mm_pbsa/mm_pbsa_readinput.pm 2007-10-09 13:25:20.000000000 -0700
@@ -530,8 +530,18 @@
die (" Results of both calculations currently need to be combined \"manually\".\n");
}
}
+ elsif($r_del->{"PROC"} == 3){
+ # Test iapbs parameters
+ &test_par(\@RL_PAR,[$r_del]);
+ &test_fil(\@RL_FIL,[$r_del,$r_pro]);
+
+ # No focussing calc for REFE > 0
+ #if($r_del->{"REFE"} > 0){
+ #die(" PB calculation with REFE > 0 doesn't work with PROC equals 2\n");
+ #}
+ }
else{
- die(" PROC parameter in PB section must be 1 or 2\n");
+ die(" PROC parameter in PB section must be 1, 2 or 3\n");
}
# Test if DIELC and INDI agree (if REFE > 0, no test is performed)
diff -ur mm_pbsa.orig/mm_pbsa_statistics.pm mm_pbsa/mm_pbsa_statistics.pm
--- mm_pbsa.orig/mm_pbsa_statistics.pm 2006-05-01 02:38:51.000000000 -0700
+++ mm_pbsa/mm_pbsa_statistics.pm 2007-10-09 13:25:20.000000000 -0700
@@ -132,6 +132,7 @@
"PB" => [1,0,'corrected reaction field energy: +(-?\d+\.\d+)'],
"PBDIS" => [1,0,'EDISPER = +(-?\d+\.\d+)'],
"PBCAV" => [1,0,'ECAVITY = +(\d+\.\d+)'],
+ "PBNONPOL" => [1,0,'ENPOLAR = +(\d+\.\d+)'],
"PBSUR" => [3,5],
"PBCAL" => [3,6],
"PBSOL" => [2,7,'+PB_PBCAL+PB_PBSUR+PB_PBDIS'],
@@ -1338,13 +1339,32 @@
}
}
elsif($calc eq "PB" && $var eq "PBSUR"){
+ # Convert PB from kT to kcal/mol
+ my $kt2kcal = $R * $TEMP / 4.184 / 1000.0;
# Calc nonpolar contribution for PB
$DATA->[$i]->{$calc}->{$var} = [];
my $j;
- for($j = 0; $j < scalar(@{$DATA->[$i]->{"PB"}->{"PBCAV"}}); $j++){
- push @{$DATA->[$i]->{$calc}->{$var}}, $gammaP * $DATA->[$i]->{"PB"}->{"PBCAV"}->[$j] + $betaP;
- }
- }
+ if (defined ($DATA->[$i]->{"PB"}->{"PBNONPOL"}->[0])){
+ for($j = 0; $j < scalar(@{$DATA->[$i]->{"PB"}->{"PBNONPOL"}}); $j++){
+ push @{$DATA->[$i]->{$calc}->{$var}}, $DATA->[$i]->{"PB"}->{"PBNONPOL"}->[$j];
+ # PBCAV and PBDIS are missing when doing iAPBS calculation
+ # zero them out so the rest of the script can proceed
+ $DATA->[$i]->{"PB"}->{"PBCAV"}->[$j] = 0.;
+ $DATA->[$i]->{"PB"}->{"PBDIS"}->[$j] = 0.;
+ print "rok INSIDE\n";
+ #print "$DATA->[$i]->{$calc}->{$var}->[$j] \n";
+ }
+ }
+ else {
+ for($j = 0; $j < scalar(@{$DATA->[$i]->{"PB"}->{"PBCAV"}}); $j++){
+ push @{$DATA->[$i]->{$calc}->{$var}}, $gammaP * $DATA->[$i]->{"PB"}->{"PBCAV"}->[$j] + $betaP;
+ # zero out PBNONPOL
+ $DATA->[$i]->{"PB"}->{"PBNONPOL"}->[$j] = 0.;
+ print "rok OUTSIDE\n";
+ }
+ }
+ }
+
# elsif($calc eq "GB" && $var eq "GBSUR"){
# # Calc nonpolar contribution for GB
# $DATA->[$i]->{$calc}->{$var} = [];
diff -ur mm_pbsa.orig/mm_pbsa_util.pm mm_pbsa/mm_pbsa_util.pm
--- mm_pbsa.orig/mm_pbsa_util.pm 2006-05-01 02:38:51.000000000 -0700
+++ mm_pbsa/mm_pbsa_util.pm 2007-10-09 13:30:21.000000000 -0700
@@ -42,6 +42,7 @@
$r_pro->{"SANDER"} = "$amberexe" . "/" . "sander";
$r_pro->{"PBSA"} = "$amberexe" . "/" . "sander"; # Was "pbsa" up to Amber9.
+ $r_pro->{"IAPBS"} = "$amberexe" . "/" . "sander.APBS";
$r_pro->{"NMODE"} = "$amberexe" . "/" . "nmode";
$r_pro->{"AMBPDB"} = "$amberexe" . "/" . "ambpdb";
$r_pro->{"MS"} = "$amberexe" . "/" . "molsurf";
@@ -67,6 +68,9 @@
elsif($r_del->{"PROC"} == 2){
unlink "pbsa.in" if(-e "pbsa.in" && ! $r_gen->{"VERBOSE"});
}
+ elsif($r_del->{"PROC"} == 3){
+ unlink "iapbs.in" if(-e "iapbs.in");
+ }
}
if( ! $r_gen->{"VERBOSE"}){

1648
contrib/iapbs/modules/Amber/patches/amber10_sander.patch Normal file
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File diff suppressed because it is too large Load Diff

297
contrib/iapbs/modules/Amber/patches/amber9_mm_pbsa.patch Normal file
View File

@@ -0,0 +1,297 @@
diff -ur mm_pbsa.orig/mm_pbsa_calceneent.pm mm_pbsa/mm_pbsa_calceneent.pm
--- mm_pbsa.orig/mm_pbsa_calceneent.pm 2007-09-14 18:36:19.000000000 -0700
+++ mm_pbsa/mm_pbsa_calceneent.pm 2007-09-26 13:56:27.000000000 -0700
@@ -57,8 +57,12 @@
print OUT "MM\n" if($r_gen->{"MM"});
print OUT "GB\n" if($r_gen->{"GB"});
print OUT "PB\n" if($r_gen->{"PB"});
- print OUT "MS\n" if($r_gen->{"GB"} || $r_gen->{"PB"} || $r_gen->{"MS"}); # Implicit use of sander/pbsa SAS
- print OUT "NM\n" if($r_gen->{"NM"}); # calc if not MS set
+ print OUT "MS\n" if($r_gen->{"GB"} ||
+ ($r_gen->{"PB"} && ($r_del->{"PROC"} != 3)) ||
+ $r_gen->{"MS"}); # Implicit use of sander/pbsa SAS
+ # calc if not MS set
+ # disabled for iAPBS (PROC=3)
+ print OUT "NM\n" if($r_gen->{"NM"});
# Parmtop file
my $npar;
@@ -129,6 +133,11 @@
my $pbsaout = "pbsa" . $suf . "." . $number . ".out";
&calc_pbsa(*OUT,"pbsa.in",$pbsaout,$ncrdfile,$npar,$r_gen,$r_pro);
}
+ elsif($r_del->{"PROC"} == 3){
+ my $pbsaout = "iapbs" . $suf . "." . $number . ".out";
+ #my $pbsain = "iapbs" . $suf . ".in";
+ &calc_iapbs(*OUT,"iapbs.in",$pbsaout,$ncrdfile,$npar,$r_gen,$r_pro,$suf);
+ }
}
# Calc MS
@@ -264,6 +273,68 @@
unlink $pbsaout;
}
+sub calc_iapbs(){
+################
+
+ # Parameters: $OUT, $pbsain, $pbsaout, $ncrdfile, $npar, $r_gen, $r_pro
+
+ my $OUT = shift;
+ my $pbsain = shift;
+ my $pbsaout = shift;
+ my $ncrdfile = shift;
+ my $npar = shift;
+ my $r_gen = shift;
+ my $r_pro = shift;
+ my $suf = shift;
+
+ print " Calc Amber/iAPBS\n";
+
+ my $command = $r_pro->{"IAPBS"} . " -O" .
+ " -i " . $pbsain .
+ " -o " . $pbsaout .
+ " -c " . $ncrdfile .
+ " -p " . $npar;
+
+
+ my $pqrfname = "";
+ $pqrfname = "com.pqr" if ($suf eq "_com");
+ $pqrfname = "rec.pqr" if ($suf eq "_rec");
+ $pqrfname = "lig.pqr" if ($suf eq "_lig");
+
+ my $lncommand = "ln -s " . $pqrfname . " ./pqr";
+ system($lncommand) && die ("Linking pqr file $pqrfname failed!\n");
+ system($command) && die(" $command not successful\n");
+ system("rm -f ./pqr");
+
+ # Write MM results
+ open(IN,"$pbsaout") || die(" $pbsaout not opened\n");
+ my $finalflg = 0;
+ my $line;
+ while(defined($line = <IN>)){
+ if($line =~ /FINAL RESULTS/){
+ $finalflg = 1;
+ }
+ elsif($finalflg > 0){
+ if ($line =~ /VDWAALS.+EEL.+EPB. += +(-?\d+\.\d+)/){
+ #print OUT $line;
+ # Convert to kT, because back-conversion to kcal/mol is done in
+ # mm_pbsa_statistics, subroutine treat_special
+ # (to be compatible with delphi calculation)
+ my $kcal2kt = 1000.0 * 4.184 / (300.0 * 8.314);
+ my $rfe = $1 * $kcal2kt;
+ printf OUT "%s %15.6f\n", "corrected reaction field energy:", $rfe;
+ }
+ elsif($line =~ /ENPOLAR +=/ && $r_gen->{"PB"} > 0 && $r_gen->{"MS"} == 0){
+ print OUT $line;
+ }
+ }
+ }
+ close(IN);
+
+ # Clean up MM
+ unlink $pbsaout;
+}
+
sub calc_delphi(){
##################
diff -ur mm_pbsa.orig/mm_pbsa_createinput.pm mm_pbsa/mm_pbsa_createinput.pm
--- mm_pbsa.orig/mm_pbsa_createinput.pm 2007-09-14 18:36:19.000000000 -0700
+++ mm_pbsa/mm_pbsa_createinput.pm 2007-09-26 13:55:26.000000000 -0700
@@ -51,6 +51,9 @@
elsif($r_del->{"PROC"} == 2){
&create_pbsa_input($r_gen, $r_san, $r_del);
}
+ elsif($r_del->{"PROC"} == 3){
+ &create_iapbs_input($r_gen, $r_san, $r_del);
+ }
}
if($r_gen->{"GC"} || $r_gen->{"AS"}){
@@ -372,7 +375,7 @@
close(OUT);
}
- }
+ }
return;
}
@@ -441,6 +444,83 @@
return;
}
+sub create_iapbs_input() {
+#########################
+ # Parameters: \%GEN,\%SAN,\%DEL
+ my $r_gen = shift;
+ my $r_san = shift;
+ my $r_del = shift;
+
+ print " iAPBS input\n";
+
+ my ($igb, $dielc, $epsin, $epsout, $istrng, $radiopt, $sprob,
+ $space, $maxitn, $npopt, $cavity_surften, $cavity_offset,
+ $srad, $bcfl, $srfm, $chgm, $swin);
+ # Do iAPBS calculation
+ $igb = 6;
+ $dielc = $r_san->{"DIELC"};
+ $epsin = $r_del->{"INDI"};
+ $epsout = $r_del->{"EXDI"};
+ my $pbions = "";
+ if(exists $r_del->{"ISTRNG"} && $r_del->{"ISTRNG"} > 0.0){
+ my $ionc = $r_del->{"ISTRNG"};
+ $pbions = " nion = 2, \n";
+ $pbions .= " ionq = 1.0, -1.0,\n";
+ $pbions .= " ionrr = 2.0, 2.0,\n";
+ $pbions .= " ionc = $ionc, $ionc,\n";
+ } else {
+ $pbions = " nion = 0,\n";
+ }
+ $radiopt = $r_del->{"RADIOPT"};
+ $sprob = $r_del->{"PRBRAD"};
+ $space = 1.0 / $r_del->{"SCALE"}->[0];
+ $srad = $r_del->{"SRAD"};
+ $bcfl = $r_del->{"BCFL"};
+ $srfm = $r_del->{"SRFM"};
+ $chgm = $r_del->{"CHGM"};
+ $swin = $r_del->{"SWIN"};
+ # ($dimex, $dimey, $dimez) = split(/,/,$r_del->{"DIME"});
+ # ($fglenx, $fgleny, $fglenz) = split(/,/,$r_del->{"FGLEN"});
+ # ($cglenx, $cgleny, $cglenz) = split(/,/,$r_del->{"CGLEN"});
+
+ my $name = "iapbs.in";
+ open(OUT,">$name") || die(" $name not opened\n");
+ print OUT "File generated by mm_pbsa.pl. Using iAPBS\n";
+ print OUT " &cntrl\n";
+ print OUT " ntf = 1, ntb = 0,\n";
+ print OUT " igb = ${igb}, dielc = ${dielc},\n";
+ print OUT " cut = 999.0, nsnb = 99999,\n";
+ print OUT " scnb = 2.0, scee = 1.2,\n";
+ print OUT " imin = 1, maxcyc = 0, ntmin = 2,\n";
+ print OUT " &end\n";
+ # Here, only REFE == 0 calculations are allowed, whereby the reference state
+ # is assumed to be INDI/INDI.
+ # Hence, only one pbsa calc with EXDI/INDI is performed,
+ # and the result taken is the reaction field energy
+ # (given as "ELE" in the pbsa output).
+ # Consider scaling of coulombic interactions as well (by DIELC) if using INDI != 1.
+ # If SALT > 0.0, only one calculation is done here (compared to delphi).
+ # For NLPB, see work of Tsui & Case, J. Phys. Chem. B 2001, 105, 11314
+ # and salt_contrib and process_phi scripts in delphi directory.
+ # Here, a PBTEMP of 300K is used to compute the Boltzmann factor for the salt effect.
+ # If a different temperature is specified here, also correct the factor for
+ # kcal/mol -> kT conversion in the subroutine calc_pbsa.
+
+ print OUT " &apbs\n";
+ print OUT " apbs_print=0, apbs_debug=0, calc_type = 0,\n";
+ print OUT " grid = ${space}, ${space}, ${space},\n";
+ print OUT " radiopt = ${radiopt}, pqr='pqr', \n";
+ print OUT " sdie = ${epsout}, pdie = ${epsin}, srad=${srad}, \n";
+ print OUT " cmeth=1, bcfl=${bcfl}, srfm=${srfm}, chgm=${chgm},\n";
+ print OUT $pbions;
+ print OUT " swin=${swin}, calcforce=0, calcnpenergy=1 \n";
+ print OUT " &end\n";
+
+ close(OUT);
+ return;
+}
+
+
sub create_makecrd_input(){
###########################
diff -ur mm_pbsa.orig/mm_pbsa_readinput.pm mm_pbsa/mm_pbsa_readinput.pm
--- mm_pbsa.orig/mm_pbsa_readinput.pm 2007-09-14 18:36:19.000000000 -0700
+++ mm_pbsa/mm_pbsa_readinput.pm 2007-09-26 14:15:39.000000000 -0700
@@ -470,8 +470,18 @@
die(" PB calculation with REFE > 0 doesn't work with PROC equals 2\n");
}
}
+ elsif($r_del->{"PROC"} == 3){
+ # Test iapbs parameters
+ &test_par(\@RL_PAR,[$r_del]);
+ &test_fil(\@RL_FIL,[$r_del,$r_pro]);
+
+ # No focussing calc for REFE > 0
+ #if($r_del->{"REFE"} > 0){
+ #die(" PB calculation with REFE > 0 doesn't work with PROC equals 2\n");
+ #}
+ }
else{
- die(" PROC parameter in PB section must be 1 or 2\n");
+ die(" PROC parameter in PB section must be 1, 2 or 3\n");
}
# Test if DIELC and INDI agree (if REFE > 0, no test is performed)
diff -ur mm_pbsa.orig/mm_pbsa_statistics.pm mm_pbsa/mm_pbsa_statistics.pm
--- mm_pbsa.orig/mm_pbsa_statistics.pm 2007-09-14 18:36:19.000000000 -0700
+++ mm_pbsa/mm_pbsa_statistics.pm 2007-09-18 12:04:03.000000000 -0700
@@ -131,6 +131,7 @@
"PB" => [1,0,'corrected reaction field energy: +(-?\d+\.\d+)'],
"PBDIS" => [1,0,'EDISPER = +(-?\d+\.\d+)'],
"PBCAV" => [1,0,'ECAVITY = +(\d+\.\d+)'],
+ "PBNONPOL" => [1,0,'ENPOLAR = +(\d+\.\d+)'],
"PBSUR" => [3,5],
"PBCAL" => [3,6],
"PBSOL" => [2,7,'+PB_PBCAL+PB_PBSUR+PB_PBDIS'],
@@ -1337,13 +1338,32 @@
}
}
elsif($calc eq "PB" && $var eq "PBSUR"){
+ # Convert PB from kT to kcal/mol
+ my $kt2kcal = $R * $TEMP / 4.184 / 1000.0;
# Calc nonpolar contribution for PB
$DATA->[$i]->{$calc}->{$var} = [];
my $j;
- for($j = 0; $j < scalar(@{$DATA->[$i]->{"PB"}->{"PBCAV"}}); $j++){
- push @{$DATA->[$i]->{$calc}->{$var}}, $gammaP * $DATA->[$i]->{"PB"}->{"PBCAV"}->[$j] + $betaP;
- }
- }
+ if (defined ($DATA->[$i]->{"PB"}->{"PBNONPOL"}->[0])){
+ for($j = 0; $j < scalar(@{$DATA->[$i]->{"PB"}->{"PBNONPOL"}}); $j++){
+ push @{$DATA->[$i]->{$calc}->{$var}}, $DATA->[$i]->{"PB"}->{"PBNONPOL"}->[$j];
+ # PBCAV and PBDIS are missing when doing iAPBS calculation
+ # zero them out so the rest of the script can proceed
+ $DATA->[$i]->{"PB"}->{"PBCAV"}->[$j] = 0.;
+ $DATA->[$i]->{"PB"}->{"PBDIS"}->[$j] = 0.;
+ print "rok INSIDE\n";
+ #print "$DATA->[$i]->{$calc}->{$var}->[$j] \n";
+ }
+ }
+ else {
+ for($j = 0; $j < scalar(@{$DATA->[$i]->{"PB"}->{"PBCAV"}}); $j++){
+ push @{$DATA->[$i]->{$calc}->{$var}}, $gammaP * $DATA->[$i]->{"PB"}->{"PBCAV"}->[$j] + $betaP;
+ # zero out PBNONPOL
+ $DATA->[$i]->{"PB"}->{"PBNONPOL"}->[$j] = 0.;
+ print "rok OUTSIDE\n";
+ }
+ }
+ }
+
# elsif($calc eq "GB" && $var eq "GBSUR"){
# # Calc nonpolar contribution for GB
# $DATA->[$i]->{$calc}->{$var} = [];
diff -ur mm_pbsa.orig/mm_pbsa_util.pm mm_pbsa/mm_pbsa_util.pm
--- mm_pbsa.orig/mm_pbsa_util.pm 2007-09-14 18:36:19.000000000 -0700
+++ mm_pbsa/mm_pbsa_util.pm 2007-09-26 14:35:01.000000000 -0700
@@ -42,6 +42,7 @@
$r_pro->{"SANDER"} = "$amberexe" . "/" . "sander";
$r_pro->{"PBSA"} = "$amberexe" . "/" . "pbsa";
+ $r_pro->{"IAPBS"} = "$amberexe" . "/" . "sander.APBS";
$r_pro->{"NMODE"} = "$amberexe" . "/" . "nmode";
$r_pro->{"AMBPDB"} = "$amberexe" . "/" . "ambpdb";
$r_pro->{"MS"} = "$amberexe" . "/" . "molsurf";
@@ -67,6 +68,9 @@
elsif($r_del->{"PROC"} == 2){
unlink "pbsa.in" if(-e "pbsa.in");
}
+ elsif($r_del->{"PROC"} == 3){
+ unlink "iapbs.in" if(-e "iapbs.in");
+ }
}
unlink "make_crd.in" if(-e "make_crd.in");
unlink "sander_com.in" if(-e "sander_com.in");

469
contrib/iapbs/modules/Amber/patches/amber9_sander.patch Normal file
View File

@@ -0,0 +1,469 @@
diff -ur sander.orig/depend sander/depend
--- sander.orig/depend 2006-04-03 16:35:54.000000000 -0700
+++ sander/depend 2007-09-25 11:54:11.000000000 -0700
@@ -187,6 +187,13 @@
amopen.o: \
copyright.h
+apbs.o: \
+ dprec.h\
+ files.h
+
+apbs_vars.o: \
+ dprec.h
+
assert.o: \
copyright.h\
assert.h
@@ -1104,6 +1111,7 @@
egb.o\
pb_force.o\
np_force.o\
+ apbs.o\
trace.o\
stack.o\
qmmm_module.o\
@@ -1149,6 +1157,7 @@
egb.LES.o\
pb_force.o\
np_force.o\
+ apbs.o\
trace.o\
stack.o\
qmmm_module.o\
@@ -1193,6 +1202,7 @@
egb.o\
pb_force.o\
np_force.o\
+ apbs.o\
trace.o\
stack.o\
qmmm_module.o\
@@ -1238,6 +1248,7 @@
egb.PIMD.o\
pb_force.o\
np_force.o\
+ apbs.o\
trace.o\
stack.o\
qmmm_module.PIMD.o\
@@ -1393,6 +1404,7 @@
pimd_vars.o\
stack.o\
nmr.o\
+ apbs.o\
box.h\
def_time.h\
ew_cntrl.h\
@@ -1431,6 +1443,7 @@
pimd_vars.o\
stack.o\
nmr.LES.o\
+ apbs.o\
box.h\
def_time.h\
ew_cntrl.h\
@@ -1473,6 +1486,7 @@
pimd_vars.o\
stack.o\
nmr.o\
+ apbs.o\
box.h\
def_time.h\
ew_cntrl.h\
@@ -1515,6 +1529,7 @@
pimd_vars.PIMD.o\
stack.o\
nmr.LES.o\
+ apbs.o\
box.h\
def_time.h\
ew_cntrl.h\
@@ -2970,6 +2985,7 @@
amoeba_runmd.o\
amoeba_mdin.o\
amoeba_interface.o\
+ apbs.o\
pimd_vars.o\
files.h\
memory.h\
@@ -3009,6 +3025,7 @@
amoeba_runmd.o\
amoeba_mdin.o\
amoeba_interface.o\
+ apbs.o\
pimd_vars.o\
files.h\
memory.h\
@@ -3052,6 +3069,7 @@
amoeba_runmd.o\
amoeba_mdin.o\
amoeba_interface.o\
+ apbs.o\
spatial_dcmp.o\
pimd_vars.o\
files.h\
@@ -3096,6 +3114,7 @@
amoeba_runmd.o\
amoeba_mdin.o\
amoeba_interface.o\
+ apbs.o\
pimd_vars.PIMD.o\
files.h\
memory.h\
diff -ur sander.orig/dynlib.f sander/dynlib.f
--- sander.orig/dynlib.f 2006-04-03 16:35:54.000000000 -0700
+++ sander/dynlib.f 2007-09-25 12:06:53.000000000 -0700
@@ -340,6 +340,10 @@
write(6,9058) eel,ehbond,econst
else if ( igb == 10 ) then
write(6,9060) eel,ehbond,econst
+#ifdef APBS
+ else if (igb == 6 .and. mdin_apbs ) then
+ write(6,9060) eel,ehbond,econst
+#endif /* APBS */
else
write(6,9059) eel,ehbond,econst
end if
@@ -374,6 +378,9 @@
end if
if (gbsa > 0) write(6,9077) esurf
if (igb == 10) write(6,9074) esurf,edisp
+#ifdef APBS
+ if (igb == 6 .and. mdin_apbs ) write(6,9087) esurf
+#endif /* APBS */
if (econst /= 0.0) write(6,9076) epot-econst
if ( dvdl /= 0.d0) write(6,9089) dvdl
#ifdef PIMD
@@ -430,6 +437,10 @@
write(7,9058) eel,ehbond,econst
else if ( igb == 10 ) then
write(7,9060) eel,ehbond,econst
+#ifdef APBS
+ else if (igb == 6 .and. mdin_apbs ) then
+ write(7,9060) eel,ehbond,econst
+#endif /* APBS */
else
write(7,9059) eel,ehbond,econst
end if
@@ -464,6 +475,9 @@
end if
if (gbsa > 0) write(7,9077) esurf
if (igb == 10) write(7,9074) esurf,edisp
+#ifdef APBS
+ if (igb == 6 .and. mdin_apbs ) write(7,9087) esurf
+#endif /* APBS */
if (econst /= 0.0) write(7,9076) epot-econst
if ( dvdl /= 0.d0) write(7,9089) dvdl
#ifndef LES
@@ -523,7 +537,7 @@
9084 format (1x,'PDDGMNDO-ESCF= ',f11.4)
9085 format (1x,'PM3CARB1-ESCF= ',f11.4)
9086 format (1x,'DFTBESCF= ',f13.4)
-
+ 9087 format (1x,'ENPOLAR= ',f14.4)
#ifdef LES
! LES and non-LES temperatures (no solvent/solute)
9068 format (1x,'T_non-LES =',f10.4,2x, 'T_LES = ',f10.4)
diff -ur sander.orig/files.h sander/files.h
--- sander.orig/files.h 2006-04-03 16:35:55.000000000 -0700
+++ sander/files.h 2007-09-12 12:50:23.000000000 -0700
@@ -45,7 +45,12 @@
logical mdin_ewald,mdin_pb,mdin_amoeba
+#ifdef APBS
+logical mdin_apbs, sp_apbs
+common/mdin_flags/mdin_ewald,mdin_pb,mdin_amoeba,mdin_apbs,sp_apbs
+#else
common/mdin_flags/mdin_ewald,mdin_pb,mdin_amoeba
+#endif /* APBS */
integer BC_HULP ! size in integers of common HULP
parameter ( BC_HULP = 9 )
diff -ur sander.orig/force.f sander/force.f
--- sander.orig/force.f 2006-04-03 16:35:55.000000000 -0700
+++ sander/force.f 2007-09-25 10:36:12.000000000 -0700
@@ -11,6 +11,9 @@
use genborn
use poisson_boltzmann, only : pb_force
use dispersion_cavity, only : npopt, np_force
+#ifdef APBS
+ use apbs
+#endif /* APBS */
use trace
use stack
use qmmm_module, only : qmmm_nml,qmmm_struct, qm2_struct, &
@@ -114,7 +117,7 @@
save ene
integer i,m,nttyp,i3
- _REAL_ virvsene,eelt,epol,esurf,edisp
+ _REAL_ virvsene,eelt,epol,esurf,edisp,enpol
_REAL_ epolar,aveper,aveind,avetot,emtot,dipiter,dipole_temp
integer l_r2x,l_rjx,l_tmp1,l_tmp2,l_tmp3,l_tmp4,l_tmp5
integer l_tmp6,l_tmp7,l_tmp8,l_jj,l_skipv, l_kvls,l_jvls,l_psi
@@ -802,6 +805,33 @@
end if ! ( igb == 10 )
+#ifdef APBS
+! APBS forces
+ if( mdin_apbs ) then
+ if (igb /= 6) then
+ write(6,*) '&apbs keyword requires igb=6.'
+ call mexit(6,1)
+ end if
+
+ call timer_start(TIME_PBFORCE)
+
+! in: coords, radii, charges
+! out: updated forces (via apbs_params) and solvation energy (pol + apolar)
+
+ if (sp_apbs) then
+ call apbs_spenergy(natom, x, f, eelt, enpol)
+ else
+ call apbs_force(natom, x, f, ene(2), eelt, enpol)
+ end if
+! ene(2) =
+! ene(3) =
+ ene(4) = eelt
+ ene(23) = enpol
+ call timer_stop(TIME_PBFORCE)
+
+ end if ! ( mdin_apbs )
+#endif /* APBS */
+
#ifdef MPI
end if
#endif
diff -ur sander.orig/Makefile sander/Makefile
--- sander.orig/Makefile 2006-04-03 16:35:54.000000000 -0700
+++ sander/Makefile 2007-09-12 12:50:23.000000000 -0700
@@ -42,6 +42,9 @@
amoeba_direct.o amoeba_mdin.o amoeba_adjust.o amoeba_self.o\
amoeba_vdw.o amoeba_induced.o amoeba_runmd.o
+APBSOBJ= \
+ apbs_vars.o apbs.o
+
QMOBJ= \
qm_mm.o qm_link_atoms.o qm_nb_list.o qm_extract_coords.o \
qm_ewald.o qm_gb.o qm_zero_charges.o qm_print_info.o \
@@ -211,6 +214,19 @@
../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB)
#---------------------------------------------------------------------------
+sander.APBS$(SFX): $(NETCDF) $(APBSOBJ) $(MMOBJ) $(QMOBJ) $(QM2OBJ) \
+ $(QMMMOBJ_DFTB) \
+ qm_div.o force.o syslib \
+ nxtsec lapack blas lmod divcon checkserconf
+ $(LOAD) -o sander.APBS$(SFX) $(APBSOBJ) $(MMOBJ) $(QMOBJ) $(QM2OBJ) \
+ $(QMMMOBJ_DFTB) \
+ qm_div.o force.o \
+ -L$(APBS_LIB) -liapbs -lapbsmainroutines -lapbs -lmaloc \
+ ../lmod/lmod.a ../dcqtp/src/qmmm/libdivcon.a $(LOADLIB) \
+ ../lapack/lapack.a ../blas/blas.a \
+ ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB)
+
+#---------------------------------------------------------------------------
psander$(SFX): $(NETCDF) $(PSOBJ) $(QMOBJ) $(QM2OBJ) $(QMMMOBJ_DFTB) \
qm_div.o force.PS.o syslib \
syslib nxtsec lapack blas lmod
diff -ur sander.orig/mdread.f sander/mdread.f
--- sander.orig/mdread.f 2006-04-03 16:35:55.000000000 -0700
+++ sander/mdread.f 2007-09-25 12:11:49.000000000 -0700
@@ -15,6 +15,9 @@
#endif
use stack, only: lastist,lastrst
use nmr, only: echoin
+#ifdef APBS
+ use apbs
+#endif /* APBS */
implicit none
# include "box.h"
# include "def_time.h"
@@ -281,6 +284,9 @@
mdin_cntrl=.false.
mdin_ewald=.false.
mdin_pb=.false.
+#ifdef APBS
+ mdin_apbs = .false.
+#endif /* APBS */
mdin_lmod=.false.
mdin_amoeba=.false.
iamoeba = 0
@@ -294,6 +300,11 @@
call nmlsrc('pb',5,ifind)
if (ifind /= 0) mdin_pb=.true.
+#ifdef APBS
+ call nmlsrc('apbs',5,ifind)
+ if (ifind /= 0) mdin_apbs=.true.
+#endif /* APBS */
+
call nmlsrc('lmod',5,ifind)
if (ifind /= 0) mdin_lmod=.true.
@@ -425,6 +436,12 @@
call pb_read
end if
+#ifdef APBS
+ if ( mdin_apbs ) then
+ call apbs_read
+ end if
+#endif /* APBS */
+
if( iamoeba == 1 ) then
if( mdin_amoeba ) then
call AMOEBA_read_mdin(5)
@@ -728,7 +745,7 @@
', iesp =',iesp
write(6,'(5x,3(a,f10.5))') 'dielc =',dielc, &
', cut =',cut,', intdiel =',intdiel
-
+
if( igb /= 0 .and. igb /= 10) then
write(6,'(5x,3(a,f10.5))') 'saltcon =',saltcon, &
', offset =',offset,', gbalpha= ',gbalpha
@@ -996,7 +1013,11 @@
write(0,*) 'GBSA=2 only works for single point energy calc'
call mexit( 6,1 )
end if
+#ifdef APBS
+ if( igb /= 0 .and. igb /= 10 .and. .not.mdin_apbs ) then
+#else
if( igb /= 0 .and. igb /= 10) then
+#endif /* APBS */
#ifdef LES
write(6,*) 'igb=1,5,7 are working with LES, no SA term included'
#endif
@@ -1289,7 +1310,7 @@
call pb_init(ifcap,natom,nres,ntypes,nbonh,nbona,ix(i02),ix(i04),ix(i06),ix(i08),ix(i10),&
ix(iibh),ix(ijbh),ix(iiba),ix(ijba),ih(m02),ih(m04),ih(m06),x(l15),x(l97))
end if ! ( igb == 10 )
-
+
if (icnstph /= 0) then
! Read charge data and alter current charges accordingly
call cnstphread(ix(icpstinf),ix(icpresst),ix(icpptcnt), &
@@ -1639,7 +1660,12 @@
write(6,'(/,a)') ' igb>0 is only compatible with ntb=0'
inerr = 1
end if
+#ifdef APBS
+ if ( ntb == 0 .and. sqrt(cut) < 8.05 .and. igb /= 10 .and. &
+ .not.mdin_apbs ) then
+#else
if ( ntb == 0 .and. sqrt(cut) < 8.05 .and. igb /= 10 ) then
+#endif /* APBS */
write(6,'(/,a,f8.2)') ' unreasonably small cut for non-periodic run: ', &
sqrt(cut)
inerr = 1
@@ -2083,7 +2109,7 @@
ih(m06),ix,x,ix(i08),ix(i10),fmn, &
nspm,ix(i70),x(l75),tmass,tmassinv,x(lmass),x(lwinv),req)
endif
-
+
! DEBUG input; force checking
call load_debug(5)
diff -ur sander.orig/printe.f sander/printe.f
--- sander.orig/printe.f 2006-04-03 16:35:55.000000000 -0700
+++ sander/printe.f 2007-09-23 21:53:02.000000000 -0700
@@ -172,6 +172,9 @@
# include "ew_mpole.h"
# include "ew_cntrl.h"
# include "tgtmd.h"
+#ifdef APBS
+# include "files.h"
+#endif /* APBS */
_REAL_ epot,enonb,enele,ehbond,ebond,eangle,edihed,enb14,eel14
_REAL_ econst,epolar,aveper,aveind,avetot,esurf,edisp,diprms,dipiter
@@ -209,6 +212,10 @@
write(6,9048) enonb,enele,ehbond
else if ( igb == 10 ) then
write(6,9050) enonb,enele,ehbond
+#ifdef APBS
+ else if ( igb == 6 .and. mdin_apbs ) then
+ write(6,9050) enonb,enele,ehbond
+#endif /* APBS */
else
write(6,9049) enonb,enele,ehbond
end if
@@ -235,6 +242,9 @@
end if
if( gbsa > 0 ) write(6,9077) esurf
if (igb == 10) write(6,9074) esurf,edisp
+#ifdef APBS
+ if (igb == 6 .and. mdin_apbs ) write(6,9069) esurf
+#endif /* APBS */
if (epolar /= 0.0) write(6,9068) epolar
if (econst /= 0.0) write(6,9078) epot-econst
if ( dvdl /= 0.d0) write(6,9089) dvdl
@@ -259,6 +269,10 @@
write(7,9048) enonb,enele,ehbond
else if ( igb == 10 ) then
write(7,9050) enonb,enele,ehbond
+#ifdef APBS
+ else if ( igb == 6 .and. mdin_apbs ) then
+ write(7,9050) enonb,enele,ehbond
+#endif /* APBS */
else
write(7,9049) enonb,enele,ehbond
end if
@@ -285,6 +299,9 @@
end if
if( gbsa > 0 ) write(7,9077) esurf
if ( igb == 10 ) write(7,9074) esurf,edisp
+#ifdef APBS
+ if (igb == 6 .and. mdin_apbs ) write(7,9069) esurf
+#endif /* APBS */
if (epolar /= 0.0) write(7,9068) epolar
if (econst /= 0.0) write(7,9078) epot-econst
if ( dvdl /= 0.d0) write(7,9089) dvdl
@@ -307,6 +324,9 @@
9058 format (1x,'1-4 VDW = ',f13.4,2x,'1-4 EEL = ',f13.4,2x, &
'RESTRAINT = ',f13.4)
9068 format (1x,'EPOLAR = ',f13.4)
+#ifdef APBS
+ 9069 format (1x,'ENPOLAR = ',f13.4)
+#endif /* APBS */
9074 format (1x,'ECAVITY = ',f13.4,2x,'EDISPER = ',f13.4)
9077 format (1x,'ESURF = ',f13.4)
9078 format (1x,'EAMBER = ',f13.4)
diff -ur sander.orig/sander.f sander/sander.f
--- sander.orig/sander.f 2006-04-03 16:35:55.000000000 -0700
+++ sander/sander.f 2007-09-25 11:01:07.000000000 -0700
@@ -34,6 +34,11 @@
use amoeba_mdin, only : beeman_integrator
use amoeba_interface, only: &
AMOEBA_deallocate,AMOEBA_readparm
+
+#ifdef APBS
+ use apbs
+#endif /* APBS */
+
#ifdef PSANDER
use spatial, only:deallocate_psander
#endif
@@ -335,6 +340,16 @@
if( igb == 0 .and. induced == 1 ) call get_dips(x,nr)
+#ifdef APBS
+! APBS initialization
+ if ( mdin_apbs ) then
+! in: natom, coords, charge and radii (from prmtop)
+! out: pb charges and pb radii (via apbs_vars module)
+ call apbs_init(natom, x(lcrd), x(l15), x(l97))
+ end if
+#endif /* APBS */
+
+
! ----- SET THE INITIAL VELOCITIES -----
if (ntx <= 3) then

22
contrib/iapbs/modules/Amber/test/2ALA/2ala.pdb Normal file
View File

@@ -0,0 +1,22 @@
ATOM 1 N ALA 1 3.326 1.548 -0.000 1.00 0.00
ATOM 2 H ALA 1 3.909 0.724 -0.000 1.00 0.00
ATOM 3 CA ALA 1 3.970 2.846 -0.000 1.00 0.00
ATOM 4 HA ALA 1 3.672 3.400 -0.890 1.00 0.00
ATOM 5 CB ALA 1 3.577 3.654 1.232 1.00 0.00
ATOM 6 1HB ALA 1 3.877 3.116 2.131 1.00 0.00
ATOM 7 2HB ALA 1 4.075 4.623 1.206 1.00 0.00
ATOM 8 3HB ALA 1 2.497 3.801 1.241 1.00 0.00
ATOM 9 C ALA 1 5.486 2.705 -0.000 1.00 0.00
ATOM 10 O ALA 1 6.009 1.593 -0.000 1.00 0.00
ATOM 11 N ALA 2 6.191 3.839 -0.000 1.00 0.00
ATOM 12 H ALA 2 5.715 4.730 -0.000 1.00 0.00
ATOM 13 CA ALA 2 7.640 3.839 -0.000 1.00 0.00
ATOM 14 HA ALA 2 8.004 3.325 0.890 1.00 0.00
ATOM 15 CB ALA 2 8.189 3.127 -1.232 1.00 0.00
ATOM 16 1HB ALA 2 7.841 3.636 -2.131 1.00 0.00
ATOM 17 2HB ALA 2 9.279 3.142 -1.206 1.00 0.00
ATOM 18 3HB ALA 2 7.841 2.094 -1.241 1.00 0.00
ATOM 19 C ALA 2 8.188 5.259 -0.000 1.00 0.00
ATOM 20 O ALA 2 7.425 6.222 0.000 1.00 0.00
TER
END

21
contrib/iapbs/modules/Amber/test/2ALA/leap.sh Normal file
View File

@@ -0,0 +1,21 @@
#!/bin/sh
#
# run tleap and generate 2ALA prm files
#
export AMBERHOME=/home/rok/src/SandBox/amber9_030906/amber9
cat > leap.input << EOF
pep = sequence { ALA ALA }
saveAmberParm pep prmtop.2ala prmcrd.2ala
savepdb pep 2ala.pdb
quit
EOF
$AMBERHOME/exe/tleap -f leap.input
rm -f leap.input

189
contrib/iapbs/modules/Amber/test/2ALA/leaprc Normal file
View File

@@ -0,0 +1,189 @@
logFile leap.log
#
# ----- leaprc for loading the ff03 (Duan et al.) force field
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "C2" "C" "sp3" }
{ "C3" "C" "sp3" }
{ "C" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "CE" "C" "sp2" }
{ "CF" "C" "sp2" }
{ "CG" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp2" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "C" "sp2" }
{ "MG" "Mg" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "F" "F" "sp3" }
{ "CL" "Cl" "sp3" }
{ "BR" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "FE" "Fe" "sp3" }
# things should be there
{ "IM" "Cl" "sp3" }
{ "IP" "Na" "sp3" }
{ "Li" "Li" "sp3" }
{ "K" "K" "sp3" }
{ "Rb" "Rb" "sp3" }
{ "Cs" "Cs" "sp3" }
{ "Zn" "Zn" "sp3" }
{ "IB" "Na" "sp3" }
# "new" types
{ "H0" "H" "sp3" }
}
#
# Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
frcmod03 = loadamberparams frcmod.ff03
#
# Load water and ions
#
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#
# Load the existing 94 lib for nucleic acids and C- and N- terminal groups
#
#
# Load DNA/RNA libraries
#
loadOff all_nucleic94.lib
#
# Load main chain and terminating
# amino acid libraries.
#
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
loadOff all_amino03.lib
#
# Define the PDB name map for the amino acids and DNA.
#
addPdbResMap {
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
{ 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
{ 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
{ 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
{ 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
{ 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" }
{ 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" }
{ 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" }
{ 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" }
{ 0 "C5" "DC5" }
{ 0 "G5" "DG5" }
{ 0 "A5" "DA5" }
{ 0 "T5" "DT5" }
{ 1 "C3" "DC3" }
{ 1 "G3" "DG3" }
{ 1 "A3" "DA3" }
{ 1 "T3" "DT3" }
}
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "H1*" "H1'" }
{ "H2*1" "H2'1" }
{ "H2*2" "H2'2" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'1" }
{ "H5*2" "H5'2" }
# old ff atom names -> new
{ "O1'" "O4'" }
{ "OA" "O1P" }
{ "OB" "O2P" }
}
#
# assumed that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE

32
contrib/iapbs/modules/Amber/test/2ALA/min-apbs.sh Normal file
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#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=min-apbs
cat > $fname <<EOF
APBS minim test
&cntrl
maxcyc=100, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug = 0, apbs_print=2,
apbs_upd_limit = 1.d-6,
dime = 33, 33, 33,
cglen = 20.0, 20.0, 20.0,
fglen = 18.0, 18.0, 16.0,
cmeth=1,
nion=2,
ionq = 1.0, -1.0,
ionc = 0.15, 0.15,
ionrr = 2.0, 2.0,
&end
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

49
contrib/iapbs/modules/Amber/test/ALA/ala-apbs.in Normal file
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@@ -0,0 +1,49 @@
read
mol pqr ala.pqr
end
elec
mg-auto
dime 33 33 33
cglen 5.9704 6.6283 5.1357
fglen 5.9704 6.6283 5.1357
cgcent mol 1
fgcent mol 1
mol 1
lpbe
bcfl sdh
pdie 2.0000
sdie 78.5400
srfm smol
chgm spl2
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
gamma 0.105
calcenergy total
calcforce no
end
elec
mg-auto
dime 33 33 33
cglen 5.9704 6.6283 5.1357
fglen 5.9704 6.6283 5.1357
cgcent mol 1
fgcent mol 1
mol 1
lpbe
bcfl sdh
pdie 2.0000
sdie 2.0000
srfm smol
chgm spl2
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
gamma 0.105
calcenergy total
calcforce no
end
print energy 2 - 1 end
quit

12
contrib/iapbs/modules/Amber/test/ALA/ala.pdb Normal file
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@@ -0,0 +1,12 @@
ATOM 1 N ALA 1 3.326 1.548 -0.000 1.00 0.00
ATOM 2 H ALA 1 3.909 0.724 -0.000 1.00 0.00
ATOM 3 CA ALA 1 3.970 2.846 -0.000 1.00 0.00
ATOM 4 HA ALA 1 3.672 3.400 -0.890 1.00 0.00
ATOM 5 CB ALA 1 3.577 3.654 1.232 1.00 0.00
ATOM 6 1HB ALA 1 3.877 3.116 2.131 1.00 0.00
ATOM 7 2HB ALA 1 4.075 4.623 1.206 1.00 0.00
ATOM 8 3HB ALA 1 2.497 3.801 1.241 1.00 0.00
ATOM 9 C ALA 1 5.486 2.705 -0.000 1.00 0.00
ATOM 10 O ALA 1 6.009 1.593 -0.000 1.00 0.00
TER
END

23
contrib/iapbs/modules/Amber/test/ALA/ala.pqr Normal file
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@@ -0,0 +1,23 @@
REMARK 1 PQR file generated by PDB2PQR (Version 1.0.2)
REMARK 1
REMARK 1 Please cite your use of PDB2PQR as:
REMARK 1 Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
REMARK 1 PDB2PQR: an automated pipeline for the setup, execution,
REMARK 1 and analysis of Poisson-Boltzmann electrostatics calculations.
REMARK 1 Nucleic Acids Research 32 W665-W667 (2004).
REMARK 1
REMARK 1 Forcefield Used: amber
REMARK 1
REMARK 5
REMARK 6 Total charge on this protein: 0.0000 e
REMARK 6
ATOM 1 N ALA 1 3.326 1.548 -0.000 -0.4157 1.8240
ATOM 2 H ALA 1 3.909 0.724 -0.000 0.2719 0.6000
ATOM 3 CA ALA 1 3.970 2.846 -0.000 0.0337 1.9080
ATOM 4 HA ALA 1 3.672 3.400 -0.890 0.0823 1.3870
ATOM 5 CB ALA 1 3.577 3.654 1.232 -0.1825 1.9080
ATOM 6 HB1 ALA 1 3.877 3.116 2.131 0.0603 1.4870
ATOM 7 HB2 ALA 1 4.075 4.623 1.206 0.0603 1.4870
ATOM 8 HB3 ALA 1 2.497 3.801 1.241 0.0603 1.4870
ATOM 9 C ALA 1 5.486 2.705 -0.000 0.5973 1.9080
ATOM 10 O ALA 1 6.009 1.593 -0.000 -0.5679 1.6612

7
contrib/iapbs/modules/Amber/test/ALA/inpcrd Normal file
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@@ -0,0 +1,7 @@
ALA
10
3.3257700 1.5479090 -0.0000016 3.9094070 0.7236110 -0.0000027
3.9700480 2.8457950 -0.0000001 3.6716630 3.4001290 -0.8898200
3.5769650 3.6538380 1.2321430 3.8774840 3.1157950 2.1311970
4.0750590 4.6230170 1.2057860 2.4969950 3.8010750 1.2413790
5.4855410 2.7052070 -0.0000044 6.0088240 1.5931750 -0.0000084

21
contrib/iapbs/modules/Amber/test/ALA/leap.sh Normal file
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#!/bin/sh
#
# run tleap and generate ALA prm files
#
export AMBERHOME=/home/rok/src/SandBox/amber9_030906/amber9
cat > leap.input << EOF
pep = sequence { ALA}
saveAmberParm pep prmtop.ala prmcrd.ala
savepdb ALA ala.pdb
quit
EOF
$AMBERHOME/exe/tleap -f leap.input
rm -f leap.input

189
contrib/iapbs/modules/Amber/test/ALA/leaprc Normal file
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logFile leap.log
#
# ----- leaprc for loading the ff03 (Duan et al.) force field
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "C2" "C" "sp3" }
{ "C3" "C" "sp3" }
{ "C" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "CE" "C" "sp2" }
{ "CF" "C" "sp2" }
{ "CG" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp2" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "C" "sp2" }
{ "MG" "Mg" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "F" "F" "sp3" }
{ "CL" "Cl" "sp3" }
{ "BR" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "FE" "Fe" "sp3" }
# things should be there
{ "IM" "Cl" "sp3" }
{ "IP" "Na" "sp3" }
{ "Li" "Li" "sp3" }
{ "K" "K" "sp3" }
{ "Rb" "Rb" "sp3" }
{ "Cs" "Cs" "sp3" }
{ "Zn" "Zn" "sp3" }
{ "IB" "Na" "sp3" }
# "new" types
{ "H0" "H" "sp3" }
}
#
# Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
frcmod03 = loadamberparams frcmod.ff03
#
# Load water and ions
#
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#
# Load the existing 94 lib for nucleic acids and C- and N- terminal groups
#
#
# Load DNA/RNA libraries
#
loadOff all_nucleic94.lib
#
# Load main chain and terminating
# amino acid libraries.
#
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
loadOff all_amino03.lib
#
# Define the PDB name map for the amino acids and DNA.
#
addPdbResMap {
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
{ 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
{ 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
{ 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
{ 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
{ 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" }
{ 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" }
{ 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" }
{ 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" }
{ 0 "C5" "DC5" }
{ 0 "G5" "DG5" }
{ 0 "A5" "DA5" }
{ 0 "T5" "DT5" }
{ 1 "C3" "DC3" }
{ 1 "G3" "DG3" }
{ 1 "A3" "DA3" }
{ 1 "T3" "DT3" }
}
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "H1*" "H1'" }
{ "H2*1" "H2'1" }
{ "H2*2" "H2'2" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'1" }
{ "H5*2" "H5'2" }
# old ff atom names -> new
{ "O1'" "O4'" }
{ "OA" "O1P" }
{ "OB" "O2P" }
}
#
# assumed that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE

32
contrib/iapbs/modules/Amber/test/ALA/md-apbs.sh Normal file
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#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=md-apbs
cat > $fname <<EOF
Example of APBS implicit solvent dynamics
&cntrl
ntx=1, irest=0, imin=0,
ntpr=1, ntwx=500, nscm=100, ntwr=5000,
dt=0.001, nstlim=50,
temp0=300, tempi=0, ntt=1, tautp=0.1,
igb=6, cut=12.0, ntb=0,
ntc=2, ntf=2, tol=0.000001
/
&apbs
apbs_debug = 0, apbs_print=0,
geom_upd_limit = 5.d-5,
dime = 33, 33, 33,
cglen = 10.0, 10.0, 10.0,
fglen = 9.0, 9.0, 9.0,
nion=2,
ionq = 1.0, -1.0,
ionc = 0.15, 0.15,
ionrr = 2.0, 2.0,
&end
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

31
contrib/iapbs/modules/Amber/test/ALA/md-pb.sh Normal file
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#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=md-pb
cat > $fname <<EOF
Sample PB implicit solvent dynamics
&cntrl
ntx=1, irest=0, imin=0,
ntpr=500, ntwx=500, nscm=100, ntwr=5000,
dt=0.001, nstlim=1000,
temp0=300, tempi=0, ntt=1, tautp=0.1,
igb=10, cut=0, ntb=0,
ntc=2, ntf=2, tol=0.000001
/
&pb
npbverb=0, nsnbr=25, nsnba=5, npbgrid=100,
npopt=0, istrng=0, epsout=80.0, epsin=1.0,
space=1., fillratio=4,
sprob=1.6, radiopt=1,
accept=0.001
/
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

21
contrib/iapbs/modules/Amber/test/ALA/md.sh Normal file
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@@ -0,0 +1,21 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=md
cat > $fname <<EOF
MD test
&cntrl
imin=0, ntx=1,
ntt=1, temp0=300.0, tautp=0.2,
ntb=0,
nstlim=5000,
ntwe=100, ntwx=100, ntpr=200,
cut=20.0, igb=0,
/
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

34
contrib/iapbs/modules/Amber/test/ALA/min-apbs.sh Normal file
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@@ -0,0 +1,34 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=min-apbs
cat > $fname <<EOF
APBS minim test
&cntrl
maxcyc=5, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug = 1, apbs_print=0,
geom_upd_limit = 1.0d-4,
evdw_upd_limit = 0.01,
dime = 33, 33, 33,
cglen = 10.0, 10.0, 10.0,
fglen = 9.0, 9.0, 9.0,
radiopt=0
cmeth=1,
nion=2,
ionq = 1.0, -1.0,
ionc = 0.15, 0.15,
ionrr = 2.0, 2.0,
&end
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

28
contrib/iapbs/modules/Amber/test/ALA/min-pb.sh Normal file
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@@ -0,0 +1,28 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=min-pb
cat > $fname <<EOF
PB test
&cntrl
maxcyc=100, imin=1,
cut=10.0,
igb=10, ntb=0,
ntpr=1,
ntx=1, irest=0, ntmin=2, ntc=1, ntf=1,
/
&pb
npbverb=1,
epsout=80.0, epsin=1.0,
istrng=0, sprob=1.6, radiopt=1,
space=0.5, nbuffer=0, accept=0.001,
cutnb=0, dbfopt=1, npopt=2,
/
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

18
contrib/iapbs/modules/Amber/test/ALA/min.sh Normal file
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@@ -0,0 +1,18 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=min
cat > $fname <<EOF
minimization test
&cntrl
maxcyc=1000, imin=1,
cut=20.0,
igb=0, ntb=0,
ntpr=1,
/
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

10
contrib/iapbs/modules/Amber/test/ALA/pbparamsin Normal file
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@@ -0,0 +1,10 @@
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0
a 0.1 1.0

153
contrib/iapbs/modules/Amber/test/ALA/prmtop Normal file
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%VERSION VERSION_STAMP = V0001.000 DATE = 03/28/06 10:51:02
%FLAG TITLE
%FORMAT(20a4)
ALA
%FLAG POINTERS
%FORMAT(10I8)
10 7 5 4 10 4 14 2 0 0
39 1 4 4 2 7 10 4 7 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
N H CA HA CB HB1 HB2 HB3 C O
%FLAG CHARGE
%FORMAT(5E16.8)
-7.37589504E+00 5.36238555E+00 -5.05359046E-01 2.20129028E+00 -4.19023611E+00
1.41091624E+00 1.41091624E+00 1.41091624E+00 1.03907928E+01 -1.01157272E+01
%FLAG MASS
%FORMAT(5E16.8)
1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.60000000E+01
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 3 4 3 5 5 5 6 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
9 4 7 6 5 3 2 1 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 2 3 5
8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
21 27 22 23 24 25 26 27 28
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ALA
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 3.40000000E+02 3.40000000E+02 3.10000000E+02 3.17000000E+02
4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.09000000E+00 1.09000000E+00 1.52600000E+00 1.52200000E+00
1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
3.50000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01
8.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.91113635E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
1.55555556E-01 0.00000000E+00 8.00000000E-01 8.00000000E-02
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
3.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
9.44293233E+05 2.12601181E+03 1.39982777E-01 9.95480466E+05 2.56678134E+03
1.04308023E+06 6.20665997E+04 5.94667300E+01 6.78771368E+04 3.25969625E+03
8.96776989E+04 1.07193646E+02 9.71708117E+04 4.98586848E+03 7.51607703E+03
8.82619071E+05 2.27577561E+03 9.24822270E+05 6.01816484E+04 8.61541883E+04
8.19971662E+05 6.06829342E+05 1.02595236E+03 6.47841731E+05 3.69471530E+04
5.44261042E+04 5.74393458E+05 3.79876399E+05
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
8.01323529E+02 2.09604198E+01 9.37598976E-02 7.36907417E+02 2.06278363E+01
6.75612247E+02 1.13252061E+02 1.93248820E+00 1.06076943E+02 1.43076527E+01
1.36131731E+02 2.59456373E+00 1.26919150E+02 1.76949863E+01 2.17257828E+01
6.53361429E+02 1.82891803E+01 5.99015525E+02 9.40505980E+01 1.12529845E+02
5.31102864E+02 6.77220874E+02 1.53505284E+01 6.26720080E+02 9.21192136E+01
1.11805549E+02 5.55666448E+02 5.64885984E+02
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
12 15 2 12 18 2 12 21 2 6
9 3 0 3 6
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
24 27 1 6 12 4 6 24 5 0
6 7
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
18 12 21 1 15 12 18 1 15 12
21 1 9 6 12 3 9 6 24 4
6 12 15 5 6 12 18 5 6 12
21 5 3 0 6 7 0 6 9 8
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 6 24 2 6 24 27 6 0 6
12 9 0 6 24 10
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
21 12 6 24 1 18 12 6 24 1
15 12 6 24 1 9 6 12 15 1
9 6 12 18 1 9 6 12 21 1
9 6 24 27 3 9 6 -24 27 4
3 0 6 9 2 3 0 6 12 2
3 0 6 24 2 0 6 12 15 1
0 6 12 18 1 0 6 12 21 1
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 6 24 27 2 0 6 24 27 2
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 9 10 3
4 5 9 4 5 6 7 8 9 10
5 6 7 8 9 10 6 7 8 9
10 7 8 9 8 9 9 10 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
N H CT H1 CT HC HC HC C O
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M E M E 3 E E E M E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.50000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01

27
contrib/iapbs/modules/Amber/test/ALA/sp-apbs.sh Normal file
View File

@@ -0,0 +1,27 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=sp-apbs
cat > $fname <<EOF
APBS SP test
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug = 5, apbs_print=1,
dime = 33, 33, 33,
cglen = 10.0, 10.0, 10.0,
fglen = 8.0, 8.0, 8.0,
sp_apbs = .TRUE.,
&end
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

28
contrib/iapbs/modules/Amber/test/ALA/sp-pb.sh Normal file
View File

@@ -0,0 +1,28 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=sp-pb
cat > $fname <<EOF
SP PB test
&cntrl
maxcyc=1, imin=1,
cut=20.0,
igb=10, ntb=0,
ntpr=1,
ntx=1, irest=0, ntmin=2, ntc=1, ntf=1,
/
&pb
npbverb=1,
epsout=80.0, epsin=1.0,
istrng=0, sprob=1.6, radiopt=1,
space=0.5, nbuffer=0, accept=0.001,
cutnb=0, dbfopt=1, npopt=2,
/
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

18
contrib/iapbs/modules/Amber/test/ALA/sp.sh Normal file
View File

@@ -0,0 +1,18 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=sp
cat > $fname <<EOF
SP test
&cntrl
maxcyc=1, imin=1,
cut=20.0,
igb=0, ntb=0,
ntpr=1,
/
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

29
contrib/iapbs/modules/Amber/test/ALA/vis-apbs.sh Normal file
View File

@@ -0,0 +1,29 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=vis-apbs
cat > $fname <<EOF
APBS visualization test
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug = 0, apbs_print=1,
dime = 33, 33, 33,
cglen = 10.0, 10.0, 10.0,
fglen = 8.0, 8.0, 8.0,
srad = 0.7,
wpot = 1, wchg = 1, wsmol = 1,
sp_apbs = .TRUE.,
&end
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

27
contrib/iapbs/modules/Amber/test/ALA/vis-pb.sh Normal file
View File

@@ -0,0 +1,27 @@
#!/bin/sh
export sander=$AMBERHOME/src/sander/sander.APBS
fname=vis-pb
cat > $fname <<EOF
Sample PB visualization input
&cntrl
ntx=1, irest=0,
imin=1, ntmin=2, maxcyc=0,
ntpr=1, igb=10, ntb=0,
ntc=1, ntf=1
/
&pb
npbverb=1, istrng=0, epsout=80.0, epsin=1.0,
space=1., accept=0.001,
sprob=1.4, cutnb=9,
phiout=1, phiform=0
/
EOF
$sander -O -i $fname -o ${fname}.out < /dev/null
rm -f $fname

20
contrib/iapbs/modules/Amber/test/Makefile Normal file
View File

@@ -0,0 +1,20 @@
#
#
#
# $Id: $
#
# this is dummy target so this Makfile doesn't fail
all:
clean::
cd apbs_radi && rm -f *.out mdin
cd Solvation && rm -f *.out
cd pbsa_pgb/iAPBS && rm -f *.out results
cd Visualization && rm -f *.out *.dx
cd smpbe && rm -f *.out *.dx
cd apbs_solv && rm -f restrt mdout mdinfo
cd Minimization && rm -f minim.out
cd mm_pbsa && make clean

22
contrib/iapbs/modules/Amber/test/Minimization/2ala.pqr Normal file
View File

@@ -0,0 +1,22 @@
ATOM 1 HH31 ACE 1 2.000 1.000 -0.000 0.1123 1.4870
ATOM 2 CH3 ACE 1 2.000 2.090 0.000 -0.3662 1.9080
ATOM 3 HH32 ACE 1 1.486 2.454 0.890 0.1123 1.4870
ATOM 4 HH33 ACE 1 1.486 2.454 -0.890 0.1123 1.4870
ATOM 5 C ACE 1 3.427 2.641 -0.000 0.5972 1.9080
ATOM 6 O ACE 1 4.391 1.877 -0.000 -0.5679 1.6612
ATOM 7 N ALA 2 3.555 3.970 -0.000 -0.4157 1.8240
ATOM 8 H ALA 2 2.733 4.556 -0.000 0.2719 0.6000
ATOM 9 CA ALA 2 4.853 4.614 -0.000 0.0337 1.9080
ATOM 10 HA ALA 2 5.408 4.316 0.890 0.0823 1.3870
ATOM 11 CB ALA 2 5.661 4.221 -1.232 -0.1825 1.9080
ATOM 12 HB1 ALA 2 5.123 4.521 -2.131 0.0603 1.4870
ATOM 13 HB2 ALA 2 6.630 4.719 -1.206 0.0603 1.4870
ATOM 14 HB3 ALA 2 5.809 3.141 -1.241 0.0603 1.4870
ATOM 15 C ALA 2 4.713 6.129 0.000 0.5973 1.9080
ATOM 16 O ALA 2 3.601 6.653 0.000 -0.5679 1.6612
ATOM 17 N NME 3 5.846 6.835 0.000 -0.4157 1.8240
ATOM 18 H NME 3 6.737 6.359 -0.000 0.2719 0.6000
ATOM 19 CH3 NME 3 5.846 8.284 0.000 -0.1490 1.9080
ATOM 20 HH31 NME 3 4.819 8.648 0.000 0.0976 1.3870
ATOM 21 HH32 NME 3 6.360 8.648 0.890 0.0976 1.3870
ATOM 22 HH33 NME 3 6.360 8.648 -0.890 0.0976 1.3870

13
contrib/iapbs/modules/Amber/test/Minimization/2ala.prmcrd Normal file
View File

@@ -0,0 +1,13 @@
ACE
22
2.0000010 1.0000000 -0.0000013 2.0000010 2.0900000 0.0000001
1.4862640 2.4538490 0.8898240 1.4862590 2.4538520 -0.8898200
3.4274200 2.6407950 -0.0000030 4.3905800 1.8774060 -0.0000066
3.5553754 3.9696488 -0.0000031 2.7331200 4.5561601 -0.0000013
4.8532621 4.6139253 -0.0000043 5.4075960 4.3155388 0.8898151
5.6613044 4.2208425 -1.2321480 5.1232615 4.5213630 -2.1312016
6.6304840 4.7189354 -1.2057908 5.8085401 3.1408723 -1.2413850
4.7126759 6.1294185 0.0000014 3.6006445 6.6527027 0.0000062
5.8460533 6.8348833 0.0000025 6.7370014 6.3591620 -0.0000004
5.8460551 8.2838837 0.0000062 4.8185761 8.6477349 0.0000104
6.3597984 8.6477313 0.8898282 6.3597900 8.6477354 -0.8898188

229
contrib/iapbs/modules/Amber/test/Minimization/2ala.prmtop Normal file
View File

@@ -0,0 +1,229 @@
%VERSION VERSION_STAMP = V0001.000 DATE = 10/18/06 21:21:36
%FLAG TITLE
%FORMAT(20a4)
ACE
%FLAG POINTERS
%FORMAT(10I8)
22 7 12 9 25 11 42 18 0 0
99 3 9 11 18 8 16 16 7 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
HH32HH33
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
1.77849648E+00 1.77849648E+00
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 1 3 4 5 6 2 7
2 1 1 1 3 4 5 6 2 7
7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
6 7 4 3 7 3 10 4 10 7
6 3 2 1 7 3 5 4 3 2
1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 2 3 5
8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
21 27 22 23 24 25 26 27 28
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ACE ALA NME
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 7 17
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
3.10000000E+02 4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
1.52600000E+00 1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01
8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01
5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01
3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00
1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 5.30000000E-01 1.50000000E-01
5.00000000E-01 8.00000000E-01 8.50000000E-01 8.00000000E-02 1.55555556E-01
7.00000000E-02 1.00000000E-01 1.70000000E+00 2.00000000E+00 1.05000000E+01
1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00
2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
6.20665997E+04 5.94667300E+01 3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.13252061E+02 1.93248820E+00 1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
3 6 3 3 9 3 0 3 3 30
33 3 30 36 3 30 39 3 24 27
5 18 21 7 54 57 5 54 60 5
54 63 5 48 51 7
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 15 1 12 18 2 3 12 4 42
45 1 42 48 2 24 30 6 24 42
4 18 24 8 48 54 8
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
12 18 21 2 9 3 12 4 6 3
9 5 6 3 12 4 0 3 6 5
0 3 9 5 0 3 12 4 42 48
51 2 36 30 39 5 33 30 36 5
33 30 39 5 27 24 30 9 27 24
42 10 24 30 33 11 24 30 36 11
24 30 39 11 21 18 24 12 18 24
27 13 60 54 63 16 57 54 60 16
57 54 63 16 51 48 54 12 48 54
57 13 48 54 60 13 48 54 63 13
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 1 12 18 24 3 3 12
15 6 3 12 18 7 45 42 48 1
42 48 54 3 30 24 42 8 24 42
45 6 24 42 48 7 18 24 30 14
18 24 42 15
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
15 12 18 21 1 15 12 -18 21 2
12 18 24 27 3 9 3 12 15 7
9 3 -12 15 3 9 3 -12 15 9
9 3 12 18 3 6 3 12 15 7
6 3 -12 15 3 6 3 -12 15 9
6 3 12 18 3 3 12 18 21 2
0 3 12 15 7 0 3 -12 15 3
0 3 -12 15 9 0 3 12 18 3
45 42 48 51 1 45 42 -48 51 2
42 48 54 57 3 42 48 54 60 3
42 48 54 63 3 39 30 24 42 10
36 30 24 42 10 33 30 24 42 10
27 24 30 33 10 27 24 30 36 10
27 24 30 39 10 27 24 42 45 7
27 24 -42 45 9 27 24 42 48 3
24 42 48 51 2 21 18 24 27 3
21 18 24 30 3 21 18 24 42 3
18 24 30 33 10 18 24 30 36 10
18 24 30 39 10 51 48 54 57 3
51 48 54 60 3 51 48 54 63 3
12 24 -18 -21 16 42 54 -48 -51 16
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 24 2 12 18 24 30 4
12 18 -24 30 3 12 18 -24 30 5
12 18 -24 30 6 12 18 24 42 7
12 18 -24 42 8 3 12 18 24 2
45 42 48 54 2 30 24 42 45 3
30 24 42 48 11 30 24 -42 48 12
24 42 48 54 2 18 24 42 45 3
18 24 42 48 13 18 24 -42 48 14
3 18 -12 -15 15 24 48 -42 -45 15
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 3 4 5 6
7 8 9 4 5 6 7 5 6 7
6 7 8 9 10 11 15 7 8 9
8 9 10 11 12 13 14 15 16 17
9 10 11 15 10 11 12 13 14 15
16 17 18 19 11 12 13 14 15 16
17 12 13 14 15 16 17 13 14 15
14 15 15 16 17 18 19 20 21 22
17 18 19 18 19 20 21 22 19 20
21 22 20 21 22 21 22 22 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1
H1 H1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E M E M E M E 3 E E E M E M E M E
E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01

12
contrib/iapbs/modules/Amber/test/Minimization/Run.apbs.min Normal file
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@@ -0,0 +1,12 @@
#!/bin/sh
export MCSH_HOME=/dev/null
output=minim.out
$AMBERHOME/bin/sander.APBS -O -i minim.in -c 2ala.prmcrd -p 2ala.prmtop -o $output
$AMBERHOME/test/dacdif $output.save $output
/bin/rm -f mdinfo restrt

20
contrib/iapbs/modules/Amber/test/Minimization/minim.in Normal file
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@@ -0,0 +1,20 @@
APBS minim test
&cntrl
maxcyc=100, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug = 0, apbs_print=0,
grid = 0.5, 0.5, 0.5,
calc_type = 0,
cmeth=1,
bcfl=2,
srfm=2,
chgm=1,
pdie=2.0,
sdie=78.54,
radiopt=2, pqr='2ala.pqr',
calcforce=2, calcnpenergy=1, calcnpforce=2,
&end

1086
contrib/iapbs/modules/Amber/test/Minimization/minim.out.save Normal file
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File diff suppressed because it is too large Load Diff

24
contrib/iapbs/modules/Amber/test/Solvation/2ala.pdb Normal file
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@@ -0,0 +1,24 @@
REMARK ACE
ATOM 1 1HH3 ACE 1 2.000 1.000 0.000
ATOM 2 CH3 ACE 1 2.000 2.090 0.000
ATOM 3 2HH3 ACE 1 1.486 2.454 0.890
ATOM 4 3HH3 ACE 1 1.486 2.454 -0.890
ATOM 5 C ACE 1 3.427 2.641 0.000
ATOM 6 O ACE 1 4.391 1.877 0.000
ATOM 7 N ALA 2 3.555 3.970 0.000
ATOM 8 H ALA 2 2.733 4.556 0.000
ATOM 9 CA ALA 2 4.853 4.614 0.000
ATOM 10 HA ALA 2 5.408 4.316 0.890
ATOM 11 CB ALA 2 5.661 4.221 -1.232
ATOM 12 1HB ALA 2 5.123 4.521 -2.131
ATOM 13 2HB ALA 2 6.630 4.719 -1.206
ATOM 14 3HB ALA 2 5.809 3.141 -1.241
ATOM 15 C ALA 2 4.713 6.129 0.000
ATOM 16 O ALA 2 3.601 6.653 0.000
ATOM 17 N NME 3 5.846 6.835 0.000
ATOM 18 H NME 3 6.737 6.359 0.000
ATOM 19 CH3 NME 3 5.846 8.284 0.000
ATOM 20 1HH3 NME 3 4.819 8.648 0.000
ATOM 21 2HH3 NME 3 6.360 8.648 0.890
ATOM 22 3HH3 NME 3 6.360 8.648 -0.890
END

43
contrib/iapbs/modules/Amber/test/Solvation/2ala.pqr Normal file
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@@ -0,0 +1,43 @@
REMARK 1 PQR file generated by PDB2PQR (Version 1.2.1)
REMARK 1
REMARK 1 Forcefield Used: amber
REMARK 1
REMARK 5
REMARK 5 WARNING: PDB2PQR was unable to assign charges
REMARK 5 to the following atoms (omitted below):
REMARK 5 1 1HH3 in ACE 1
REMARK 5 3 2HH3 in ACE 1
REMARK 5 4 3HH3 in ACE 1
REMARK 5 20 1HH3 in NME 3
REMARK 5 21 2HH3 in NME 3
REMARK 5 22 3HH3 in NME 3
REMARK 5
REMARK 5 WARNING: Non-integral net charges were found in
REMARK 5 the following residues:
REMARK 5 ACE A 1 - Residue Charge: -0.3369
REMARK 5 NME A 3 - Residue Charge: -0.2928
REMARK 5
REMARK 6 Total charge on this protein: -0.6297 e
REMARK 6
ATOM 1 1HH3 ACE 1 2.000 1.000 0.000 0.1123 1.487
ATOM 2 CH3 ACE 1 2.000 2.090 0.000 -0.3662 1.9080
ATOM 3 2HH3 ACE 1 1.486 2.454 0.890 0.1123 1.487
ATOM 4 3HH3 ACE 1 1.486 2.454 -0.890 0.1123 1.487
ATOM 5 C ACE 1 3.427 2.641 0.000 0.5972 1.9080
ATOM 6 O ACE 1 4.391 1.877 0.000 -0.5679 1.6612
ATOM 7 N ALA 2 3.555 3.970 0.000 -0.4157 1.8240
ATOM 8 H ALA 2 2.733 4.556 0.000 0.2719 0.6000
ATOM 9 CA ALA 2 4.853 4.614 0.000 0.0337 1.9080
ATOM 10 HA ALA 2 5.408 4.316 0.890 0.0823 1.3870
ATOM 11 CB ALA 2 5.661 4.221 -1.232 -0.1825 1.9080
ATOM 12 HB1 ALA 2 5.123 4.521 -2.131 0.0603 1.4870
ATOM 13 HB2 ALA 2 6.630 4.719 -1.206 0.0603 1.4870
ATOM 14 HB3 ALA 2 5.809 3.141 -1.241 0.0603 1.4870
ATOM 15 C ALA 2 4.713 6.129 0.000 0.5973 1.9080
ATOM 16 O ALA 2 3.601 6.653 0.000 -0.5679 1.6612
ATOM 17 N NME 3 5.846 6.835 0.000 -0.4157 1.8240
ATOM 18 H NME 3 6.737 6.359 0.000 0.2719 0.6000
ATOM 19 CH3 NME 3 5.846 8.284 0.000 -0.1490 1.9080
ATOM 20 1HH3 NME 3 4.819 8.648 0.000 0.0976 1.387
ATOM 21 2HH3 NME 3 6.360 8.648 0.890 0.0976 1.387
ATOM 22 3HH3 NME 3 6.360 8.648 -0.890 0.0976 1.387

13
contrib/iapbs/modules/Amber/test/Solvation/2ala.prmcrd Normal file
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@@ -0,0 +1,13 @@
ACE
22
2.0000010 1.0000000 -0.0000013 2.0000010 2.0900000 0.0000001
1.4862640 2.4538490 0.8898240 1.4862590 2.4538520 -0.8898200
3.4274200 2.6407950 -0.0000030 4.3905800 1.8774060 -0.0000066
3.5553754 3.9696488 -0.0000031 2.7331200 4.5561601 -0.0000013
4.8532621 4.6139253 -0.0000043 5.4075960 4.3155388 0.8898151
5.6613044 4.2208425 -1.2321480 5.1232615 4.5213630 -2.1312016
6.6304840 4.7189354 -1.2057908 5.8085401 3.1408723 -1.2413850
4.7126759 6.1294185 0.0000014 3.6006445 6.6527027 0.0000062
5.8460533 6.8348833 0.0000025 6.7370014 6.3591620 -0.0000004
5.8460551 8.2838837 0.0000062 4.8185761 8.6477349 0.0000104
6.3597984 8.6477313 0.8898282 6.3597900 8.6477354 -0.8898188

229
contrib/iapbs/modules/Amber/test/Solvation/2ala.prmtop Normal file
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@@ -0,0 +1,229 @@
%VERSION VERSION_STAMP = V0001.000 DATE = 10/18/06 21:21:36
%FLAG TITLE
%FORMAT(20a4)
ACE
%FLAG POINTERS
%FORMAT(10I8)
22 7 12 9 25 11 42 18 0 0
99 3 9 11 18 8 16 16 7 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
HH32HH33
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
1.77849648E+00 1.77849648E+00
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 1 3 4 5 6 2 7
2 1 1 1 3 4 5 6 2 7
7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
6 7 4 3 7 3 10 4 10 7
6 3 2 1 7 3 5 4 3 2
1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 2 3 5
8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
21 27 22 23 24 25 26 27 28
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ACE ALA NME
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 7 17
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
3.10000000E+02 4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
1.52600000E+00 1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01
8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01
5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01
3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00
1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 5.30000000E-01 1.50000000E-01
5.00000000E-01 8.00000000E-01 8.50000000E-01 8.00000000E-02 1.55555556E-01
7.00000000E-02 1.00000000E-01 1.70000000E+00 2.00000000E+00 1.05000000E+01
1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00
2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
6.20665997E+04 5.94667300E+01 3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.13252061E+02 1.93248820E+00 1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
3 6 3 3 9 3 0 3 3 30
33 3 30 36 3 30 39 3 24 27
5 18 21 7 54 57 5 54 60 5
54 63 5 48 51 7
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 15 1 12 18 2 3 12 4 42
45 1 42 48 2 24 30 6 24 42
4 18 24 8 48 54 8
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
12 18 21 2 9 3 12 4 6 3
9 5 6 3 12 4 0 3 6 5
0 3 9 5 0 3 12 4 42 48
51 2 36 30 39 5 33 30 36 5
33 30 39 5 27 24 30 9 27 24
42 10 24 30 33 11 24 30 36 11
24 30 39 11 21 18 24 12 18 24
27 13 60 54 63 16 57 54 60 16
57 54 63 16 51 48 54 12 48 54
57 13 48 54 60 13 48 54 63 13
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 1 12 18 24 3 3 12
15 6 3 12 18 7 45 42 48 1
42 48 54 3 30 24 42 8 24 42
45 6 24 42 48 7 18 24 30 14
18 24 42 15
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
15 12 18 21 1 15 12 -18 21 2
12 18 24 27 3 9 3 12 15 7
9 3 -12 15 3 9 3 -12 15 9
9 3 12 18 3 6 3 12 15 7
6 3 -12 15 3 6 3 -12 15 9
6 3 12 18 3 3 12 18 21 2
0 3 12 15 7 0 3 -12 15 3
0 3 -12 15 9 0 3 12 18 3
45 42 48 51 1 45 42 -48 51 2
42 48 54 57 3 42 48 54 60 3
42 48 54 63 3 39 30 24 42 10
36 30 24 42 10 33 30 24 42 10
27 24 30 33 10 27 24 30 36 10
27 24 30 39 10 27 24 42 45 7
27 24 -42 45 9 27 24 42 48 3
24 42 48 51 2 21 18 24 27 3
21 18 24 30 3 21 18 24 42 3
18 24 30 33 10 18 24 30 36 10
18 24 30 39 10 51 48 54 57 3
51 48 54 60 3 51 48 54 63 3
12 24 -18 -21 16 42 54 -48 -51 16
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 24 2 12 18 24 30 4
12 18 -24 30 3 12 18 -24 30 5
12 18 -24 30 6 12 18 24 42 7
12 18 -24 42 8 3 12 18 24 2
45 42 48 54 2 30 24 42 45 3
30 24 42 48 11 30 24 -42 48 12
24 42 48 54 2 18 24 42 45 3
18 24 42 48 13 18 24 -42 48 14
3 18 -12 -15 15 24 48 -42 -45 15
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 3 4 5 6
7 8 9 4 5 6 7 5 6 7
6 7 8 9 10 11 15 7 8 9
8 9 10 11 12 13 14 15 16 17
9 10 11 15 10 11 12 13 14 15
16 17 18 19 11 12 13 14 15 16
17 12 13 14 15 16 17 13 14 15
14 15 15 16 17 18 19 20 21 22
17 18 19 18 19 20 21 22 19 20
21 22 20 21 22 21 22 22 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1
H1 H1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E M E M E M E 3 E E E M E M E M E
E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
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%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01

22
contrib/iapbs/modules/Amber/test/Solvation/APBS/2ala.pqr Normal file
View File

@@ -0,0 +1,22 @@
ATOM 1 HH31 ACE 1 2.000 1.000 -0.000 0.1123 1.4870
ATOM 2 CH3 ACE 1 2.000 2.090 0.000 -0.3662 1.9080
ATOM 3 HH32 ACE 1 1.486 2.454 0.890 0.1123 1.4870
ATOM 4 HH33 ACE 1 1.486 2.454 -0.890 0.1123 1.4870
ATOM 5 C ACE 1 3.427 2.641 -0.000 0.5972 1.9080
ATOM 6 O ACE 1 4.391 1.877 -0.000 -0.5679 1.6612
ATOM 7 N ALA 2 3.555 3.970 -0.000 -0.4157 1.8240
ATOM 8 H ALA 2 2.733 4.556 -0.000 0.2719 0.6000
ATOM 9 CA ALA 2 4.853 4.614 -0.000 0.0337 1.9080
ATOM 10 HA ALA 2 5.408 4.316 0.890 0.0823 1.3870
ATOM 11 CB ALA 2 5.661 4.221 -1.232 -0.1825 1.9080
ATOM 12 HB1 ALA 2 5.123 4.521 -2.131 0.0603 1.4870
ATOM 13 HB2 ALA 2 6.630 4.719 -1.206 0.0603 1.4870
ATOM 14 HB3 ALA 2 5.809 3.141 -1.241 0.0603 1.4870
ATOM 15 C ALA 2 4.713 6.129 0.000 0.5973 1.9080
ATOM 16 O ALA 2 3.601 6.653 0.000 -0.5679 1.6612
ATOM 17 N NME 3 5.846 6.835 0.000 -0.4157 1.8240
ATOM 18 H NME 3 6.737 6.359 -0.000 0.2719 0.6000
ATOM 19 CH3 NME 3 5.846 8.284 0.000 -0.1490 1.9080
ATOM 20 HH31 NME 3 4.819 8.648 0.000 0.0976 1.3870
ATOM 21 HH32 NME 3 6.360 8.648 0.890 0.0976 1.3870
ATOM 22 HH33 NME 3 6.360 8.648 -0.890 0.0976 1.3870

73
contrib/iapbs/modules/Amber/test/Solvation/APBS/notes.txt Normal file
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@@ -0,0 +1,73 @@
= APBS reference run =
Last modified: 09/24/07 19:25:03 (rok)
== Run ==
../../../bin/apbs solvation-apbs.in | tee solvation-apbs.out
== Results ==
=== In solvent ===
- APBS
PRINT STATEMENTS
print energy 1 (elec) end
Local net energy (PE 0) = 1.028311368153E+03 kJ/mol
Global net ELEC energy = 1.028311368153E+03 kJ/mol
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148317453106E+01 kJ/mol
1028.311368153 / 4.184 = 245.77231552 kcal/mol
41.48317453106 / 4.184 = 9.91471666 kcal/mol
- iAPBS/sander (in debug directory):
iAPBS: Electrostatic energy in solvent: 245.720 kcal/mol
iAPBS: Nonpolar energy in solvent: 9.916 kcal/mol
=== In vacuum ===
- APBS
print energy 1 (elec) end
Local net energy (PE 0) = 1.089755873935E+03 kJ/mol
Global net ELEC energy = 1.089755873935E+03 kJ/mol
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148317453106E+01 kJ/mol
1089.755873935 / 4.184 = 260.45790486 kcal/mol
- iAPBS/sander
iAPBS: Electrostatic energy in vacuum: 260.395 kcal/mol
iAPBS: Nonpolar energy in vacuum: 0.000 kcal/mol
=== Difference (Solvation energy) ===
- APBS
1089.755873935 - 1028.311368153 = 61.444505782 kJ/mol = 14.68558933 kcal/mol
245.77231552 - 260.45790486 = -14.68558934 kcal/mol
- iAPBS/sander
VDWAALS = 2.8120 EEL = -80.1238 EPB = -14.6754
ENPOLAR = 9.9161

48
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs-debug.in Normal file
View File

@@ -0,0 +1,48 @@
read
mol pqr 2ala.pqr
end
elec name elec
mg-manual
dime 33 33 33
grid 0.500 0.500 0.500
nlev 4
gcent mol 1
pdie 2.000
sdie 78.540
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl sdh
srfm spl2
calcenergy total
calcforce comps
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
print elecForce elec end
print apolforce npolar end
print elecEnergy elec end
print apolEnergy npolar end
quit

313
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs-debug.out.save Normal file
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@@ -0,0 +1,313 @@
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 0.5.1
Nathan A. Baker (baker@biochem.wustl.edu)
Dept. Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2002-2007. Washington University in St. Louis.
All Rights Reserved.
Portions Copyright (c) 1999-2002. The Regents of the University of
California.
Portions Copyright (c) 1995. Michael Holst.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Linking APBS statically or dynamically with other modules is making a
combined work based on APBS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
SPECIAL GPL EXCEPTION
In addition, as a special exception, the copyright holders of APBS
give you permission to combine the APBS program with free software
programs and libraries that are released under the GNU LGPL or with
code included in releases of ISIM, Ion Simulator Interface, PMV,
SMOL, VMD, and Vision. Such combined software may be linked with APBS and
redistributed together in original or modified form as mere aggregation
without requirement that the entire work be under the scope of the GNU
General Public License. This special exception permission is also extended
to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG,
FEtk, MC, or MALOC libraries.
Note that people who make modified versions of APBS are not obligated
to grant this special exception for their modified versions; it is
their choice whether to do so. The GNU General Public License gives
permission to release a modified version without this exception; this
exception also makes it possible to release a modified version which
carries forward this exception.
----------------------------------------------------------------------
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 written in an object-oriented
version of C. It 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
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 Sep 12 2007 at 10:43:13
Parsing input file solvation-apbs-debug.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from 2ala.pqr.
22 atoms
Centered at (4.112e+00, 4.824e+00, -6.205e-01)
Net charge -2.78e-17 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.500 x 0.500 x 0.500
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (4.112, 4.824, -0.620)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 2.000
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
----------------------------------------
CALCULATION #2 (npolar): APOLAR
----------------------------------------
PRINT STATEMENTS
print force 1 (elec) 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 -2.578360181314E+00 1.875838438673E+01 2.608987274422E+00
ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 0 -1.112553258645E-01 1.485287039149E-01 3.088566500048E-03
tot 0 -2.689615507179E+00 1.890691309065E+01 2.612075840922E+00
qf 1 -2.386463926127E+01 6.114406244708E+00 3.454679294373E+01
ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 1 1.024031341873E-02 -5.756474123361E-02 -1.060083237180E-01
tot 1 -2.385439894785E+01 6.056841503475E+00 3.444078462001E+01
qf 2 2.384642488245E+00 -2.334127350216E+00 -1.179273572110E+01
ib 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 2 1.400862696540E-01 -2.533696207811E-01 -5.259101369873E-01
tot 2 2.524728757899E+00 -2.587496970997E+00 -1.231864585808E+01
qf 3 2.529734707044E+00 -2.583809826643E+00 1.268562212627E+01
ib 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 3 1.296867099294E-01 -1.728678114544E-01 1.856076068664E-01
tot 3 2.659421416973E+00 -2.756677638097E+00 1.287122973313E+01
qf 4 -7.366071516960E+00 -1.230021593870E+02 8.650534852267E+01
ib 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 4 -3.567837127287E-01 4.581480231499E-01 -1.477496164304E+00
tot 4 -7.722855229688E+00 -1.225440113639E+02 8.502785235836E+01
qf 5 -1.279540956351E+02 1.066868136208E+02 8.855350282503E+01
ib 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 5 -8.304310479546E+00 8.783491534764E+00 2.238743345837E+00
tot 5 -1.362584061147E+02 1.154703051556E+02 9.079224617087E+01
qf 6 -8.193154481610E+01 3.637713460551E+01 4.829497227004E+01
ib 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 6 6.333199151754E+00 -4.651256740826E+00 2.022976119138E+00
tot 6 -7.559834566435E+01 3.172587786468E+01 5.031794838917E+01
qf 7 5.104203284201E+01 -1.618936859389E+01 1.488051239702E+01
ib 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 7 1.558245747882E-01 -1.564956598998E-01 2.096164352218E-01
tot 7 5.119785741679E+01 -1.634586425379E+01 1.509012883224E+01
qf 8 -1.895229717461E+00 -5.179212957913E+00 -1.528313605966E+00
ib 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 8 -3.363269946584E-01 -2.883115743689E-01 -8.449156324465E-01
tot 8 -2.231556712119E+00 -5.467524532282E+00 -2.373229238412E+00
qf 9 -8.504910430912E-01 -3.303183403763E+00 1.651578789462E+00
ib 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 9 -3.814186261833E-01 -3.341877524550E-01 -6.340417012566E-01
tot 9 -1.231909669275E+00 -3.637371156218E+00 1.017537088206E+00
qf 10 7.654500618919E+00 -6.568373643510E+00 -1.099903433105E+01
ib 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 10 2.962983357408E-03 -8.913420645841E-02 -7.881947521953E-02
tot 10 7.657463602276E+00 -6.657507849968E+00 -1.107785380627E+01
qf 11 2.359451338193E+00 -1.143940330945E+00 3.447849052849E+00
ib 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 11 1.252194702939E-01 -1.766767061342E-01 6.452119069862E-02
tot 11 2.484670808487E+00 -1.320617037079E+00 3.512370243548E+00
qf 12 -3.437143242848E+00 -4.072139789580E+00 -1.277033099522E+00
ib 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 12 -4.270869598182E-01 -6.184088658548E-01 -6.647630015389E-01
tot 12 -3.864230202666E+00 -4.690548655435E+00 -1.941796101061E+00
qf 13 -1.132007029655E+00 3.272185341312E+00 -4.617425899208E-02
ib 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 13 2.960083358873E-01 1.168355578113E+00 -6.239211120350E-01
tot 13 -8.359986937675E-01 4.440540919425E+00 -6.700953710271E-01
qf 14 2.258916940392E+01 2.046566115524E+01 9.176737059115E+01
ib 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 14 2.513454159109E-01 1.459425658709E-01 -2.649740154572E+00
tot 14 2.284051481983E+01 2.061160372112E+01 8.911763043658E+01
qf 15 8.360258194437E+01 -1.597146614711E+02 9.000566287802E+01
ib 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 15 1.071503438932E+01 -7.209757019942E+00 3.040758947418E+00
tot 15 9.431761633369E+01 -1.669244184910E+02 9.304642182543E+01
qf 16 1.524768557897E+01 -7.642400634382E+01 4.507362582378E+01
ib 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 16 -3.046631204025E+01 1.072150987328E+01 -2.095776281218E-01
tot 16 -1.521862646128E+01 -6.570249647054E+01 4.486404819566E+01
qf 17 4.415109459290E+00 3.389714685944E+01 2.047990031931E+01
ib 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 17 -4.875103612823E+00 3.478351703110E-01 1.268224001035E-01
tot 17 -4.599941535336E-01 3.424498202975E+01 2.060672271941E+01
qf 18 4.447227271244E+00 1.644522892295E+01 6.388402412066E+00
ib 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 18 9.504506631115E-02 8.163302830437E-02 -8.054671455404E-02
tot 18 4.542272337555E+00 1.652686195126E+01 6.307855697512E+00
qf 19 6.877904277249E+00 -7.514330614280E+00 2.132560466296E+00
ib 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 19 1.186552778933E+00 2.718809958544E-01 8.245848349065E-02
tot 19 8.064457056182E+00 -7.242449618425E+00 2.215018949787E+00
qf 20 -3.815629032910E+00 -6.943343885511E+00 -4.537432267182E+00
ib 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 20 -2.571651427165E-01 -4.506994382582E-02 -2.507235162311E-01
tot 20 -4.072794175627E+00 -6.988413829337E+00 -4.788155783413E+00
qf 21 -3.723380254707E+00 -6.564742643809E+00 5.598196411919E+00
ib 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 21 -7.558087939836E-02 -1.354588154284E-01 1.564756990480E-01
tot 21 -3.798961134105E+00 -6.700201459238E+00 5.754672110967E+00
tot all -8.154869011643E+01 -1.715816730904E+02 5.244247670536E+02
print APOL force 1 (npolar) 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 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sasa 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sasa 2 -1.881066742799E+01 -6.019413576958E-01 1.926212344627E+01
sav 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 2 -1.881066742799E+01 -6.019413576958E-01 1.926212344627E+01
sasa 3 -1.941260878569E+01 -1.655338733663E+00 -1.775727005203E+01
sav 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 3 -1.941260878569E+01 -1.655338733663E+00 -1.775727005203E+01
sasa 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sav 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sasa 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sav 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sasa 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sav 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sasa 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sav 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sasa 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sav 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sasa 10 2.410412977298E+01 -1.106419071547E+01 -2.133808209412E+01
sav 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 10 2.410412977298E+01 -1.106419071547E+01 -2.133808209412E+01
sasa 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sav 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sasa 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sav 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sasa 13 1.850969674915E+01 -1.610193131836E+01 -1.143688579622E+01
sav 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 13 1.850969674915E+01 -1.610193131836E+01 -1.143688579622E+01
sasa 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sav 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sasa 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sav 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sasa 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sav 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sasa 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 18 4.346646352505E+00 4.267616418823E+01 3.951496684096E-01
sav 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 18 4.346646352505E+00 4.267616418823E+01 3.951496684096E-01
sasa 19 -1.654842130919E+01 2.468239110523E+01 0.000000000000E+00
sav 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 19 -1.654842130919E+01 2.468239110523E+01 0.000000000000E+00
sasa 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sav 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sasa 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
sav 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
tot all 1.006446977549E+01 2.143586264522E+01 2.668403298113E+00
print energy 1 (elec) end
Local net energy (PE 0) = 1.028311368153E+03 kJ/mol
Global net ELEC energy = 1.028311368153E+03 kJ/mol
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148317453106E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Final memory usage: 8.454 MB total, 8.667 MB high water
Thanks for using APBS!

48
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs-vac-debug.in Normal file
View File

@@ -0,0 +1,48 @@
read
mol pqr 2ala.pqr
end
elec name elec
mg-manual
dime 33 33 33
grid 0.500 0.500 0.500
nlev 4
gcent mol 1
pdie 2.000
sdie 1.00
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl sdh
srfm spl2
calcenergy total
calcforce comps
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
print elecForce elec end
print apolforce npolar end
print elecEnergy elec end
print apolEnergy npolar end
quit

313
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs-vac-debug.out.save Normal file
View File

@@ -0,0 +1,313 @@
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 0.5.1
Nathan A. Baker (baker@biochem.wustl.edu)
Dept. Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2002-2007. Washington University in St. Louis.
All Rights Reserved.
Portions Copyright (c) 1999-2002. The Regents of the University of
California.
Portions Copyright (c) 1995. Michael Holst.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Linking APBS statically or dynamically with other modules is making a
combined work based on APBS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
SPECIAL GPL EXCEPTION
In addition, as a special exception, the copyright holders of APBS
give you permission to combine the APBS program with free software
programs and libraries that are released under the GNU LGPL or with
code included in releases of ISIM, Ion Simulator Interface, PMV,
SMOL, VMD, and Vision. Such combined software may be linked with APBS and
redistributed together in original or modified form as mere aggregation
without requirement that the entire work be under the scope of the GNU
General Public License. This special exception permission is also extended
to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG,
FEtk, MC, or MALOC libraries.
Note that people who make modified versions of APBS are not obligated
to grant this special exception for their modified versions; it is
their choice whether to do so. The GNU General Public License gives
permission to release a modified version without this exception; this
exception also makes it possible to release a modified version which
carries forward this exception.
----------------------------------------------------------------------
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 written in an object-oriented
version of C. It 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
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 Sep 12 2007 at 10:43:13
Parsing input file solvation-apbs-vac-debug.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from 2ala.pqr.
22 atoms
Centered at (4.112e+00, 4.824e+00, -6.205e-01)
Net charge -2.78e-17 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.500 x 0.500 x 0.500
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (4.112, 4.824, -0.620)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 2.000
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
----------------------------------------
CALCULATION #2 (npolar): APOLAR
----------------------------------------
PRINT STATEMENTS
print force 1 (elec) 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 6.281531888568E-01 1.854065155912E+01 2.601074818912E+00
ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 0 3.978670072302E-01 -2.955501678650E-01 8.437566864254E-03
tot 0 1.026020196087E+00 1.824510139126E+01 2.609512385776E+00
qf 1 -3.207752850281E+01 1.290548520883E+01 3.474050266118E+01
ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 1 8.279312685094E-02 -6.130512335850E-02 1.776396612354E-02
tot 1 -3.199473537596E+01 1.284418008547E+01 3.475826662730E+01
qf 2 3.640819124527E+00 -4.227619662527E+00 -1.249140754411E+01
ib 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 2 -3.803208461395E-02 5.128921540299E-02 1.248824363217E-01
tot 2 3.602787039913E+00 -4.176330447124E+00 -1.236652510779E+01
qf 3 3.824667021045E+00 -4.415893300564E+00 1.321390767889E+01
ib 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 3 -3.745462415223E-02 4.914202559273E-02 -1.326407042979E-01
tot 3 3.787212396892E+00 -4.366751274971E+00 1.308126697459E+01
qf 4 1.522075369197E+01 -1.440108764898E+02 8.632147965005E+01
ib 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 4 2.030767269246E-01 -3.584099546484E-01 1.232547759522E-01
tot 4 1.542383041889E+01 -1.443692864444E+02 8.644473442600E+01
qf 5 -1.537063794172E+02 1.370291645540E+02 8.684144824573E+01
ib 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 5 2.123927217121E+00 -2.439202362842E+00 6.170719625099E-01
tot 5 -1.515824522001E+02 1.345899621912E+02 8.745852020824E+01
qf 6 -9.356291508109E+01 4.346618757585E+01 4.915716177506E+01
ib 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 6 -2.503855324163E+00 1.753622795155E+00 -1.898465801595E-02
tot 6 -9.606677040525E+01 4.521981037101E+01 4.913817711705E+01
qf 7 7.726933036804E+01 -1.877624592318E+01 1.606406530828E+01
ib 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 7 -1.169197849371E-01 8.923760189439E-02 -3.018267164292E-02
tot 7 7.715241058311E+01 -1.868700832129E+01 1.603388263663E+01
qf 8 -2.443495416567E+00 -5.737917678027E+00 -1.814748525434E+00
ib 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 8 1.028296687587E-01 -1.062752474568E-01 1.689674823910E-01
tot 8 -2.340665747808E+00 -5.844192925484E+00 -1.645781043043E+00
qf 9 -2.776309828221E+00 -6.049952556061E+00 2.785679768683E-01
ib 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 9 2.613971809668E-01 -4.503768624191E-01 3.431175126559E-01
tot 9 -2.514912647255E+00 -6.500329418480E+00 6.216854895242E-01
qf 10 1.040829795858E+01 -1.477498160536E+00 -1.056169984492E+01
ib 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 10 7.803585070708E-02 -7.881841344928E-02 5.961861704021E-02
tot 10 1.048633380929E+01 -1.556316573985E+00 -1.050208122788E+01
qf 11 1.886612704424E+00 -2.155915536500E+00 3.653356391714E+00
ib 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 11 -5.379874191468E-02 3.656434367407E-02 -3.874817966881E-02
tot 11 1.832813962509E+00 -2.119351192826E+00 3.614608212045E+00
qf 12 -4.589758090567E+00 -5.985997827646E+00 -2.262135898805E+00
ib 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 12 4.713429967783E-01 3.555339814866E-01 3.630350857632E-01
tot 12 -4.118415093788E+00 -5.630463846160E+00 -1.899100813042E+00
qf 13 -2.178337475994E+00 7.837800424267E-01 6.699601634927E-01
ib 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 13 8.437945422216E-02 -6.730905540050E-01 1.679489122962E-01
tot 13 -2.093958021772E+00 1.106894884217E-01 8.379090757888E-01
qf 14 -3.478917654185E+00 3.274531596988E+01 8.826058570314E+01
ib 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 14 -3.211275274981E-01 1.449884122095E-01 1.484963357034E-01
tot 14 -3.800045181683E+00 3.289030438209E+01 8.840908203884E+01
qf 15 1.136014888745E+02 -1.824151429142E+02 9.157163006266E+01
ib 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 15 -3.773072304527E+00 2.815398569426E-01 -1.102074587349E-02
tot 15 1.098284165699E+02 -1.821336030572E+02 9.156060931678E+01
qf 16 3.584635943075E+01 -8.556117773390E+01 4.632179727081E+01
ib 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 16 2.707625367578E+00 -1.087607703804E+00 1.833388674637E-01
tot 16 3.855398479833E+01 -8.664878543770E+01 4.650513613827E+01
qf 17 -3.128648152641E+01 4.903088438960E+01 1.832384450185E+01
ib 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 17 1.245177643423E-01 -4.822564750973E-02 -7.875600562191E-03
tot 17 -3.116196376207E+01 4.898265874209E+01 1.831596890129E+01
qf 18 8.713235777586E+00 1.714284629384E+01 6.445699283183E+00
ib 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 18 -9.131631309058E-02 2.587722524915E-03 5.780803000813E-03
tot 18 8.621919464496E+00 1.714543401637E+01 6.451480086184E+00
qf 19 3.647949487435E+00 -1.004992529255E+01 2.106345970750E+00
ib 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 19 -6.381310633539E-01 -2.750669343433E-03 2.419154933592E-03
tot 19 3.009818424081E+00 -1.005267596190E+01 2.108765125683E+00
qf 20 -5.748601577339E+00 -7.560561256258E+00 -4.799757889654E+00
ib 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 20 3.557735298313E-02 6.150668525524E-02 1.350188563218E-01
tot 20 -5.713024224356E+00 -7.499054571002E+00 -4.664739033332E+00
qf 21 -5.657437325902E+00 -7.248744005541E+00 5.737056824424E+00
ib 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 21 3.430523651614E-02 6.097777255684E-02 -1.362183049517E-01
tot 21 -5.623132089386E+00 -7.187766232984E+00 5.600838519473E+00
tot all -6.368452708591E+01 -1.767437750376E+02 5.224722160544E+02
print APOL force 1 (npolar) 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 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sasa 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sasa 2 -1.881066742799E+01 -6.019413576958E-01 1.926212344627E+01
sav 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 2 -1.881066742799E+01 -6.019413576958E-01 1.926212344627E+01
sasa 3 -1.941260878569E+01 -1.655338733663E+00 -1.775727005203E+01
sav 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 3 -1.941260878569E+01 -1.655338733663E+00 -1.775727005203E+01
sasa 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sav 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sasa 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sav 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sasa 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sav 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sasa 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sav 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sasa 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sav 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sasa 10 2.410412977298E+01 -1.106419071547E+01 -2.133808209412E+01
sav 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 10 2.410412977298E+01 -1.106419071547E+01 -2.133808209412E+01
sasa 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sav 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sasa 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sav 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sasa 13 1.850969674915E+01 -1.610193131836E+01 -1.143688579622E+01
sav 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 13 1.850969674915E+01 -1.610193131836E+01 -1.143688579622E+01
sasa 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sav 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sasa 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sav 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sasa 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sav 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sasa 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 18 4.346646352505E+00 4.267616418823E+01 3.951496684096E-01
sav 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 18 4.346646352505E+00 4.267616418823E+01 3.951496684096E-01
sasa 19 -1.654842130919E+01 2.468239110523E+01 0.000000000000E+00
sav 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 19 -1.654842130919E+01 2.468239110523E+01 0.000000000000E+00
sasa 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sav 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sasa 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
sav 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
tot all 1.006446977549E+01 2.143586264522E+01 2.668403298113E+00
print energy 1 (elec) end
Local net energy (PE 0) = 1.089755873935E+03 kJ/mol
Global net ELEC energy = 1.089755873935E+03 kJ/mol
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148317453106E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Final memory usage: 8.454 MB total, 8.667 MB high water
Thanks for using APBS!

45
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs-vac.in Normal file
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read
mol pqr 2ala.pqr
end
elec name elec
mg-manual
dime 33 33 33
grid 0.500 0.500 0.500
nlev 4
gcent mol 1
pdie 2.000
sdie 1.0
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl sdh
srfm spl2
calcenergy total
calcforce comps
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
print elecEnergy elec end
print apolEnergy npolar end
quit

118
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs-vac.out.save Normal file
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----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 0.5.1
Nathan A. Baker (baker@biochem.wustl.edu)
Dept. Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2002-2007. Washington University in St. Louis.
All Rights Reserved.
Portions Copyright (c) 1999-2002. The Regents of the University of
California.
Portions Copyright (c) 1995. Michael Holst.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Linking APBS statically or dynamically with other modules is making a
combined work based on APBS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
SPECIAL GPL EXCEPTION
In addition, as a special exception, the copyright holders of APBS
give you permission to combine the APBS program with free software
programs and libraries that are released under the GNU LGPL or with
code included in releases of ISIM, Ion Simulator Interface, PMV,
SMOL, VMD, and Vision. Such combined software may be linked with APBS and
redistributed together in original or modified form as mere aggregation
without requirement that the entire work be under the scope of the GNU
General Public License. This special exception permission is also extended
to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG,
FEtk, MC, or MALOC libraries.
Note that people who make modified versions of APBS are not obligated
to grant this special exception for their modified versions; it is
their choice whether to do so. The GNU General Public License gives
permission to release a modified version without this exception; this
exception also makes it possible to release a modified version which
carries forward this exception.
----------------------------------------------------------------------
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 written in an object-oriented
version of C. It 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
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 Sep 12 2007 at 10:43:13
Parsing input file solvation-apbs-vac.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from 2ala.pqr.
22 atoms
Centered at (4.112e+00, 4.824e+00, -6.205e-01)
Net charge -2.78e-17 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.500 x 0.500 x 0.500
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (4.112, 4.824, -0.620)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 2.000
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
----------------------------------------
CALCULATION #2 (npolar): APOLAR
----------------------------------------
PRINT STATEMENTS
print energy 1 (elec) end
Local net energy (PE 0) = 1.089755873935E+03 kJ/mol
Global net ELEC energy = 1.089755873935E+03 kJ/mol
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148317453106E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Final memory usage: 8.454 MB total, 8.664 MB high water
Thanks for using APBS!

45
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs.in Normal file
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@@ -0,0 +1,45 @@
read
mol pqr 2ala.pqr
end
elec name elec
mg-manual
dime 33 33 33
grid 0.500 0.500 0.500
nlev 4
gcent mol 1
pdie 2.000
sdie 78.540
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl sdh
srfm spl2
calcenergy total
calcforce comps
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
print elecEnergy elec end
print apolEnergy npolar end
quit

118
contrib/iapbs/modules/Amber/test/Solvation/APBS/solvation-apbs.out.save Normal file
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----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 0.5.1
Nathan A. Baker (baker@biochem.wustl.edu)
Dept. Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2002-2007. Washington University in St. Louis.
All Rights Reserved.
Portions Copyright (c) 1999-2002. The Regents of the University of
California.
Portions Copyright (c) 1995. Michael Holst.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Linking APBS statically or dynamically with other modules is making a
combined work based on APBS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
SPECIAL GPL EXCEPTION
In addition, as a special exception, the copyright holders of APBS
give you permission to combine the APBS program with free software
programs and libraries that are released under the GNU LGPL or with
code included in releases of ISIM, Ion Simulator Interface, PMV,
SMOL, VMD, and Vision. Such combined software may be linked with APBS and
redistributed together in original or modified form as mere aggregation
without requirement that the entire work be under the scope of the GNU
General Public License. This special exception permission is also extended
to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG,
FEtk, MC, or MALOC libraries.
Note that people who make modified versions of APBS are not obligated
to grant this special exception for their modified versions; it is
their choice whether to do so. The GNU General Public License gives
permission to release a modified version without this exception; this
exception also makes it possible to release a modified version which
carries forward this exception.
----------------------------------------------------------------------
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 written in an object-oriented
version of C. It 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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
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 Sep 12 2007 at 10:43:13
Parsing input file solvation-apbs.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from 2ala.pqr.
22 atoms
Centered at (4.112e+00, 4.824e+00, -6.205e-01)
Net charge -2.78e-17 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.500 x 0.500 x 0.500
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (4.112, 4.824, -0.620)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 2.000
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
----------------------------------------
CALCULATION #2 (npolar): APOLAR
----------------------------------------
PRINT STATEMENTS
print energy 1 (elec) end
Local net energy (PE 0) = 1.028311368153E+03 kJ/mol
Global net ELEC energy = 1.028311368153E+03 kJ/mol
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148317453106E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Final memory usage: 8.454 MB total, 8.664 MB high water
Thanks for using APBS!

13
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ACE
22
2.0000010 1.0000000 -0.0000013 2.0000010 2.0900000 0.0000001
1.4862640 2.4538490 0.8898240 1.4862590 2.4538520 -0.8898200
3.4274200 2.6407950 -0.0000030 4.3905800 1.8774060 -0.0000066
3.5553754 3.9696488 -0.0000031 2.7331200 4.5561601 -0.0000013
4.8532621 4.6139253 -0.0000043 5.4075960 4.3155388 0.8898151
5.6613044 4.2208425 -1.2321480 5.1232615 4.5213630 -2.1312016
6.6304840 4.7189354 -1.2057908 5.8085401 3.1408723 -1.2413850
4.7126759 6.1294185 0.0000014 3.6006445 6.6527027 0.0000062
5.8460533 6.8348833 0.0000025 6.7370014 6.3591620 -0.0000004
5.8460551 8.2838837 0.0000062 4.8185761 8.6477349 0.0000104
6.3597984 8.6477313 0.8898282 6.3597900 8.6477354 -0.8898188

229
contrib/iapbs/modules/Amber/test/Solvation/PBSA/2ala.prmtop Normal file
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%VERSION VERSION_STAMP = V0001.000 DATE = 10/18/06 21:21:36
%FLAG TITLE
%FORMAT(20a4)
ACE
%FLAG POINTERS
%FORMAT(10I8)
22 7 12 9 25 11 42 18 0 0
99 3 9 11 18 8 16 16 7 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
HH32HH33
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
1.77849648E+00 1.77849648E+00
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 1 3 4 5 6 2 7
2 1 1 1 3 4 5 6 2 7
7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
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6 3 2 1 7 3 5 4 3 2
1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
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8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
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%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ACE ALA NME
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 7 17
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
3.10000000E+02 4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
1.52600000E+00 1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
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8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01
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%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00
1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
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%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 5.30000000E-01 1.50000000E-01
5.00000000E-01 8.00000000E-01 8.50000000E-01 8.00000000E-02 1.55555556E-01
7.00000000E-02 1.00000000E-01 1.70000000E+00 2.00000000E+00 1.05000000E+01
1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00
2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
6.20665997E+04 5.94667300E+01 3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.13252061E+02 1.93248820E+00 1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
3 6 3 3 9 3 0 3 3 30
33 3 30 36 3 30 39 3 24 27
5 18 21 7 54 57 5 54 60 5
54 63 5 48 51 7
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 15 1 12 18 2 3 12 4 42
45 1 42 48 2 24 30 6 24 42
4 18 24 8 48 54 8
%FLAG ANGLES_INC_HYDROGEN
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12 18 21 2 9 3 12 4 6 3
9 5 6 3 12 4 0 3 6 5
0 3 9 5 0 3 12 4 42 48
51 2 36 30 39 5 33 30 36 5
33 30 39 5 27 24 30 9 27 24
42 10 24 30 33 11 24 30 36 11
24 30 39 11 21 18 24 12 18 24
27 13 60 54 63 16 57 54 60 16
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%FLAG ANGLES_WITHOUT_HYDROGEN
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15 12 18 1 12 18 24 3 3 12
15 6 3 12 18 7 45 42 48 1
42 48 54 3 30 24 42 8 24 42
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%FORMAT(10I8)
15 12 18 21 1 15 12 -18 21 2
12 18 24 27 3 9 3 12 15 7
9 3 -12 15 3 9 3 -12 15 9
9 3 12 18 3 6 3 12 15 7
6 3 -12 15 3 6 3 -12 15 9
6 3 12 18 3 3 12 18 21 2
0 3 12 15 7 0 3 -12 15 3
0 3 -12 15 9 0 3 12 18 3
45 42 48 51 1 45 42 -48 51 2
42 48 54 57 3 42 48 54 60 3
42 48 54 63 3 39 30 24 42 10
36 30 24 42 10 33 30 24 42 10
27 24 30 33 10 27 24 30 36 10
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27 24 -42 45 9 27 24 42 48 3
24 42 48 51 2 21 18 24 27 3
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18 24 30 39 10 51 48 54 57 3
51 48 54 60 3 51 48 54 63 3
12 24 -18 -21 16 42 54 -48 -51 16
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 24 2 12 18 24 30 4
12 18 -24 30 3 12 18 -24 30 5
12 18 -24 30 6 12 18 24 42 7
12 18 -24 42 8 3 12 18 24 2
45 42 48 54 2 30 24 42 45 3
30 24 42 48 11 30 24 -42 48 12
24 42 48 54 2 18 24 42 45 3
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3 18 -12 -15 15 24 48 -42 -45 15
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 3 4 5 6
7 8 9 4 5 6 7 5 6 7
6 7 8 9 10 11 15 7 8 9
8 9 10 11 12 13 14 15 16 17
9 10 11 15 10 11 12 13 14 15
16 17 18 19 11 12 13 14 15 16
17 12 13 14 15 16 17 13 14 15
14 15 15 16 17 18 19 20 21 22
17 18 19 18 19 20 21 22 19 20
21 22 20 21 22 21 22 22 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1
H1 H1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E M E M E M E 3 E E E M E M E M E
E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
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0 0 0 0 0 0 0 0 0 0
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%FLAG IROTAT
%FORMAT(10I8)
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%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
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8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
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8.50000000E-01 8.50000000E-01

6
contrib/iapbs/modules/Amber/test/Solvation/PBSA/Run.sh Normal file
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#!/bin/sh
$AMBERHOME/exe/sander -O -i solvation-pbsa.in \
-c 2ala.prmcrd -p 2ala.prmtop -o solvation-pbsa.out

14
contrib/iapbs/modules/Amber/test/Solvation/PBSA/solvation-pbsa.in Normal file
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APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=10, ntb=0,
ntpr=1,
/
&pb
npbverb=1, istrng=0, epsout=78.54, epsin=1.0,
sprob=1.4, radiopt=1, npopt=2,
space=0.5, nbuffer=0, accept=0.001,
cutnb=0, dbfopt=1, fillratio=3.0,
&end

373
contrib/iapbs/modules/Amber/test/Solvation/PBSA/solvation-pbsa.out.save Normal file
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-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 09/24/2007 at 20:07:29
[-O]verwriting output
File Assignments:
| MDIN: solvation-pbsa.in
| MDOUT: solvation-pbsa.out
|INPCRD: 2ala.prmcrd
| PARM: 2ala.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=10, ntb=0,
ntpr=1,
/
&pb
npbverb=1, istrng=0, epsout=78.54, epsin=1.0,
sprob=1.4, radiopt=1, npopt=2,
space=0.5, nbuffer=0, accept=0.001,
cutnb=0, dbfopt=1, fillratio=3.0,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 10/18/06 Time = 21:21:36
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 42 MPHIA = 18
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 18 NUMBND = 8
NUMANG = 16 NPTRA = 16 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 1592
| Hollerith 137
| Integer 21004
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 95 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 10, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
======== Implicit Solvent Initialization ========
Max Nonbonded Pairs: 243 243 243
no. of atoms processed in PB initialization: 22
NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
1 ACE HH31 HC 0.112300 0.000000 0.000000 0.000000 1.324766
2 ACE CH3 CT -0.366200 -0.029300 0.567900 2.250000 1.699835
3 ACE HH32 HC 0.112300 0.000000 0.000000 0.000000 1.324766
4 ACE HH33 HC 0.112300 0.000000 0.000000 0.000000 1.324766
5 ACE C C 0.597200 0.597200 -0.143800 2.000000 1.699835
6 ACE O O -0.567900 -0.567900 0.029300 1.570000 1.479961
7 ALA N N -0.415700 -0.143800 0.569400 1.950000 1.624999
8 ALA H H 0.271900 0.000000 0.000000 0.000000 0.534539
9 ALA CA CT 0.033700 0.116000 0.567900 2.250000 1.699835
10 ALA HA H1 0.082300 0.000000 0.000000 0.000000 1.235677
11 ALA CB CT -0.182500 -0.001600 0.114400 2.250000 1.699835
12 ALA HB1 HC 0.060300 0.000000 0.000000 0.000000 1.324766
13 ALA HB2 HC 0.060300 0.000000 0.000000 0.000000 1.324766
14 ALA HB3 HC 0.060300 0.000000 0.000000 0.000000 1.324766
15 ALA C C 0.597300 0.597300 0.001600 2.000000 1.699835
16 ALA O O -0.567900 -0.567900 0.029400 1.570000 1.479961
17 NME N N -0.415700 -0.143800 0.597300 1.950000 1.624999
18 NME H H 0.271900 0.000000 0.000000 0.000000 0.534539
19 NME CH3 CT -0.149000 0.143800 0.000000 2.250000 1.699835
20 NME HH31 H1 0.097600 0.000000 0.000000 0.000000 1.235677
21 NME HH32 H1 0.097600 0.000000 0.000000 0.000000 1.235677
22 NME HH33 H1 0.097600 0.000000 0.000000 0.000000 1.235677
total system charges (+/-) for PB 0.0000 2.6649 -2.6649
cavity_surften = 0.0436 cavity_offset = -1.0080
SAS Surface: surface dots generated: 366
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NB-update: residue-based nb list 133
NB-update: atom-based nb list 231
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 4.000 5.000 -0.500
Xmin, Xmax, Xmax-Xmin: -0.250 8.096 8.346
Ymin, Ymax, Ymax-Ymin: -0.160 10.534 10.694
Zmin, Zmax, Zmax-Zmin: -3.482 2.250 5.732
beginning box center at level 1 4.000 5.000 -0.500
beginning box center at level 2 4.000 5.000 -0.500
Grid dimension at level 1 7 9 5
Grid origin corrected at level 1 -12.000 -15.000 -12.500
Grid dimension at level 2 31 35 25
Grid origin corrected at level 2 -4.000 -4.000 -7.000
SA surface: setting up working radii
SA surface: found nonzero radii 10
Number of SA srf points exposed 905
Number of SA arcs generated 45
Number of SA arc points exposed 386 with resolution (A)
0.250000000000000
Atomic solvent accessible surface area:
2 101.089670559196
5 4.36595542984129
6 26.6516652256658
7 9.24761273571448
9 18.7541922756880
11 69.5277372171847
15 4.36595542984129
16 27.8631045541051
17 13.8714191035717
19 104.749025149574
======== FDPB Summary ========
Do FDPB every 1 steps
Nonbonded Update
residue cutoff is set to 12.0000000000000
fdpb cutoff is set to 5.00000000000000
sas cutoff is set to 9.00000000000000
nonbonded cutoff is set to 0.000000000000000E+000
Grid Constants
Grid dimension 7 9 5
Grid spacing set to 4.00000000000000
Grid boundary
-12.000 16.000
-15.000 21.000
-12.500 7.500
Dielectric Map
Use Tan, Yang, and Luo optimized cavity radii definition
Use probe-accessible surface definition
Compute SAS every 1 steps
Solvent probe radius 1.40000000000000
Surface dots per atom 366
Buried atom radii increment 0.800000000000000
Threshhold for exposed atom 0.200000000000000
Current SAS 380.486337680383
Boundary conditions
sum of grid charges as independent DH spheres
Physical constants
Solute dielectric constant : 1.00000000000000
Solvent dielectric constant : 78.5400000000000
Temperature (K) : 300.000000000000
Ionic strength (mM) : 0.000000000000000E+000
Debye-Huckel parameter (1/A): 0.000000000000000E+000
FD Solver Option
Use Modified ICCG solver
Iteration data
Maximum iterations : 100
Convergence criteria: 1.000000000000000E-003
Iterations required : 5
Norm of the constant vector: 39.4802024250119
Norm of the residual vector: 3.721685067021821E-002
Convergence achieved : 9.426712221374068E-004
======== FDPB Summary ========
Do FDPB every 1 steps
Nonbonded Update
residue cutoff is set to 12.0000000000000
fdpb cutoff is set to 5.00000000000000
sas cutoff is set to 9.00000000000000
nonbonded cutoff is set to 0.000000000000000E+000
Grid Constants
Grid dimension 31 35 25
Grid spacing set to 0.500000000000000
Grid boundary
-4.000 11.500
-4.000 13.500
-7.000 5.500
Dielectric Map
Use Tan, Yang, and Luo optimized cavity radii definition
Use probe-accessible surface definition
Compute SAS every 1 steps
Solvent probe radius 1.40000000000000
Surface dots per atom 366
Buried atom radii increment 0.800000000000000
Threshhold for exposed atom 0.200000000000000
Current SAS 380.486337680383
Boundary conditions
electrostatic focus boundary condition
Physical constants
Solute dielectric constant : 1.00000000000000
Solvent dielectric constant : 78.5400000000000
Temperature (K) : 300.000000000000
Ionic strength (mM) : 0.000000000000000E+000
Debye-Huckel parameter (1/A): 0.000000000000000E+000
FD Solver Option
Use Modified ICCG solver
Iteration data
Maximum iterations : 100
Convergence criteria: 1.000000000000000E-003
Iterations required : 16
Norm of the constant vector: 10398.4392644656
Norm of the residual vector: 7.23488893769438
Convergence achieved : 6.957668120847726E-004
Total surface charge -0.0001
Reaction field energy -13.6451
SA surface: setting up working radii
SA surface: found nonzero radii 22
Number of SA srf points exposed 1379
Number of SA arcs generated 189
Number of SA arc points exposed 644 with resolution (A)
0.250000000000000
Atomic solvent accessible surface area:
1 31.6088730480371
2 2.63934311259723
3 31.6088730480371
4 31.6088730480371
5 4.28893255727052
6 28.7622827195504
7 5.34106970749324
8 0.000000000000000E+000
9 0.329917889074654
10 17.8885136949356
11 2.63934311259723
12 25.2361163851264
13 23.1968342529950
14 18.3535391891829
15 3.95901466824972
16 31.3252584074311
17 11.3105005570445
18 0.000000000000000E+000
19 7.91802933779170
20 20.0351353383279
21 30.5297300393568
22 30.5297300393568
Cavity solvation energy 14.6348
Dispersion solvation energy -18.0035
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.1885E+01 6.0661E+00 2.1987E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -13.6451
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ECAVITY = 14.6348 EDISPER = -18.0035
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.1885E+01 6.0661E+00 2.1987E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -13.6451
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ECAVITY = 14.6348 EDISPER = -18.0035
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.61% of Total)
| Fast Water setup 0.00 ( 0.02% of Total)
| PB NB list 0.00 ( 0.18% of PB No)
| PB FD Setup 0.00 ( 4.16% of PB No)
| PB Solver 0.02 (69.33% of PB FD)
| PB Sas/Eps 0.01 (22.76% of PB FD)
| Other 0.00 ( 7.91% of PB FD)
| PB FD Force 0.02 (95.57% of PB No)
| PB Direct 0.00 ( 0.07% of PB No)
| Other 0.00 ( 0.02% of PB No)
| PB Nonbond 0.02 (86.00% of Nonbo)
| NP Sas 0.00 (46.60% of NP No)
| NP Cavity 0.00 ( 0.13% of NP No)
| NP Dispersion 0.00 (53.22% of NP No)
| Other 0.00 ( 0.05% of NP No)
| NP Nonbond 0.00 (14.00% of Nonbo)
| Nonbond force 0.03 (99.61% of Force)
| Bond/Angle/Dihedral 0.00 ( 0.36% of Force)
| Other 0.00 ( 0.04% of Force)
| Force time 0.03 (100.0% of Runmd)
| Runmd Time 0.03 (89.73% of Total)
| Other 0.00 ( 9.64% of Total)
| Total time 0.03 (99.79% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 20:07:29.044 on 09/24/2007
| Setup done at 20:07:29.047 on 09/24/2007
| Run done at 20:07:29.075 on 09/24/2007
| wallclock() was called 50 times

20
contrib/iapbs/modules/Amber/test/Solvation/Run.apbs.solv Normal file
View File

@@ -0,0 +1,20 @@
#!/bin/sh
export MCSH_HOME=/dev/null
output=solvation.out
$AMBERHOME/bin/sander.APBS -O -i solvation.in \
-c 2ala.prmcrd -p 2ala.prmtop -o $output
$AMBERHOME/test/dacdif $output.save $output
output=solvation-auto.out
$AMBERHOME/bin/sander.APBS -O -i solvation-auto.in \
-c 2ala.prmcrd -p 2ala.prmtop -o $output
$AMBERHOME/test/dacdif $output.save $output
/bin/rm -f mdinfo restrt

24
contrib/iapbs/modules/Amber/test/Solvation/debug/solvation-auto.in Normal file
View File

@@ -0,0 +1,24 @@
APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=9,
apbs_print=1,
fglen= 13.801, 18.154, 10.192,
cglen= 13.801, 18.154 10.192,
dime= 33, 33, 33,
calc_type=1,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
&end

384
contrib/iapbs/modules/Amber/test/Solvation/debug/solvation-auto.log Normal file
View File

@@ -0,0 +1,384 @@
debug: Input string:
read
mol pqr ion.pqr
end
elec name elec
mg-auto
dime 33 33 33
cglen 13.801 18.154 10.192
fglen 13.801 18.154 10.192
cgcent mol 1
fgcent mol 1
pdie 1.000
sdie 78.540
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl mdh
srfm smol
calcenergy total
calcforce no
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
quit
Parsed input string.
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.431 x 0.567 x 0.319
Grid lengths: 13.801 x 18.154 x 10.192
Grid center: (4.112, 4.824, -0.621)
Multigrid levels: 4
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
----------------------------------------
CALCULATION #2 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.431 x 0.567 x 0.319
Grid lengths: 13.801 x 18.154 x 10.192
Grid center: (4.112, 4.824, -0.621)
Multigrid levels: 4
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
----------------------------------------
CALCULATION #3 (npolar): APOLAR
energyAPOL: 41.489065
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148906464712E+01 kJ/mol
print APOL force 1 (npolar) 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 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sasa 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sasa 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sav 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sasa 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sav 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sasa 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sav 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sasa 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sav 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sasa 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sav 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sasa 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sav 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sasa 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sav 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sasa 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sav 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sasa 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sav 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sasa 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sav 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sasa 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sav 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sasa 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sav 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sasa 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sav 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sasa 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sav 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sasa 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sav 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sasa 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sav 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sasa 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sav 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sasa 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
sav 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
tot all 1.010028716361E+01 2.172761646898E+01 2.668403298113E+00
----------------------------------------
Final memory usage: 8.695 MB total, 8.961 MB high water
debug: Input string:
read
mol pqr ion.pqr
end
elec name elec
mg-auto
dime 33 33 33
cglen 13.801 18.154 10.192
fglen 13.801 18.154 10.192
cgcent mol 1
fgcent mol 1
pdie 1.000
sdie 1.000
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl mdh
srfm smol
calcenergy total
calcforce no
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
quit
Parsed input string.
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.431 x 0.567 x 0.319
Grid lengths: 13.801 x 18.154 x 10.192
Grid center: (4.112, 4.824, -0.621)
Multigrid levels: 4
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
----------------------------------------
CALCULATION #2 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.431 x 0.567 x 0.319
Grid lengths: 13.801 x 18.154 x 10.192
Grid center: (4.112, 4.824, -0.621)
Multigrid levels: 4
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
----------------------------------------
CALCULATION #3 (npolar): APOLAR
energyAPOL: 41.489065
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148906464712E+01 kJ/mol
print APOL force 1 (npolar) 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 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sasa 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sasa 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sav 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sasa 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sav 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sasa 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sav 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sasa 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sav 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sasa 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sav 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sasa 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sav 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sasa 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sav 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sasa 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sav 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sasa 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sav 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sasa 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sav 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sasa 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sav 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sasa 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sav 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sasa 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sav 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sasa 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sav 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sasa 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sav 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sasa 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sav 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sasa 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sav 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sasa 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
sav 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
tot all 1.010028716361E+01 2.172761646898E+01 2.668403298113E+00
----------------------------------------
Final memory usage: 17.209 MB total, 17.477 MB high water

392
contrib/iapbs/modules/Amber/test/Solvation/debug/solvation-auto.out Normal file
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-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 09/24/2007 at 22:02:40
[-O]verwriting output
File Assignments:
| MDIN: solvation-auto.in
| MDOUT: Ba
|INPCRD: 2ala.prmcrd
| PARM: 2ala.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=9,
apbs_print=1,
fglen= 13.801, 18.154, 10.192,
cglen= 13.801, 18.154 10.192,
dime= 33, 33, 33,
calc_type=1,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 10/18/06 Time = 21:21:36
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 42 MPHIA = 18
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 18 NUMBND = 8
NUMANG = 16 NPTRA = 16 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 1592
| Hollerith 137
| Integer 21004
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 95 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 6, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
iAPBS: Initializing APBS interface
iAPBS: Reading radii definition from pqr filename: 2ala.pqr
APBS calculation parameters:
Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Smoothed molecular surface definition.
Using cubic B-spline discretization
Grid dimension: 33 33 33
Coarse grid lengths: 13.801 18.154 10.192
Fine grid lengths: 13.801 18.154 10.192
Solute dielectric (pdie): 1.000
Solvent dielectric (sdie): 78.540
Temperature: 298.150
Surface sphere density (sdens): 10.000
Surface tension: 0.105
radiopt is set to 3
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
iAPBS: unpacked coordinates, charge and radius:
1 2.000 1.000 0.000 0.112 1.487
2 2.000 2.090 0.000 -0.366 1.908
3 1.486 2.454 0.890 0.112 1.487
4 1.486 2.454 -0.890 0.112 1.487
5 3.427 2.641 0.000 0.597 1.908
6 4.391 1.877 0.000 -0.568 1.661
7 3.555 3.970 0.000 -0.416 1.824
8 2.733 4.556 0.000 0.272 0.600
9 4.853 4.614 0.000 0.034 1.908
10 5.408 4.316 0.890 0.082 1.387
11 5.661 4.221 -1.232 -0.182 1.908
12 5.123 4.521 -2.131 0.060 1.487
13 6.630 4.719 -1.206 0.060 1.487
14 5.809 3.141 -1.241 0.060 1.487
15 4.713 6.129 0.000 0.597 1.908
16 3.601 6.653 0.000 -0.568 1.661
17 5.846 6.835 0.000 -0.416 1.824
18 6.737 6.359 0.000 0.272 0.600
19 5.846 8.284 0.000 -0.149 1.908
20 4.819 8.648 0.000 0.098 1.387
21 6.360 8.648 0.890 0.098 1.387
22 6.360 8.648 -0.890 0.098 1.387
iAPBS: Calling apbsdrv
iAPBS: apbs return code: 0
iAPBS: apbs return code: 0
iAPBS: TotalForces: 1 4.108 0.761 -0.017
iAPBS: TotalForces: 2 6.437 8.400 0.055
iAPBS: TotalForces: 3 0.126 -1.054 -1.019
iAPBS: TotalForces: 4 0.162 -1.035 0.979
iAPBS: TotalForces: 5 -10.816 -5.205 3.291
iAPBS: TotalForces: 6 -15.856 -9.593 9.277
iAPBS: TotalForces: 7 -1.998 -18.943 -5.755
iAPBS: TotalForces: 8 1.173 1.094 -0.176
iAPBS: TotalForces: 9 8.610 9.436 1.432
iAPBS: TotalForces: 10 -0.417 -0.207 1.012
iAPBS: TotalForces: 11 0.958 -4.145 -7.140
iAPBS: TotalForces: 12 0.424 -0.661 -1.502
iAPBS: TotalForces: 13 1.974 -4.806 -3.120
iAPBS: TotalForces: 14 9.767 6.261 -7.979
iAPBS: TotalForces: 15 -1.239 0.475 7.502
iAPBS: TotalForces: 16 -5.177 -1.051 -0.431
iAPBS: TotalForces: 17 -1.541 8.188 3.810
iAPBS: TotalForces: 18 -3.350 -2.477 -0.165
iAPBS: TotalForces: 19 6.599 4.841 -0.004
iAPBS: TotalForces: 20 0.937 6.805 -0.022
iAPBS: TotalForces: 21 -0.437 1.472 0.515
iAPBS: TotalForces: 22 -0.447 1.444 -0.543
iAPBS: SolventForces: 1 0.000 0.000 0.000
iAPBS: SolventForces: 2 0.000 0.000 0.000
iAPBS: SolventForces: 3 0.000 0.000 0.000
iAPBS: SolventForces: 4 0.000 0.000 0.000
iAPBS: SolventForces: 5 0.000 0.000 0.000
iAPBS: SolventForces: 6 0.000 0.000 0.000
iAPBS: SolventForces: 7 0.000 0.000 0.000
iAPBS: SolventForces: 8 0.000 0.000 0.000
iAPBS: SolventForces: 9 0.000 0.000 0.000
iAPBS: SolventForces: 10 0.000 0.000 0.000
iAPBS: SolventForces: 11 0.000 0.000 0.000
iAPBS: SolventForces: 12 0.000 0.000 0.000
iAPBS: SolventForces: 13 0.000 0.000 0.000
iAPBS: SolventForces: 14 0.000 0.000 0.000
iAPBS: SolventForces: 15 0.000 0.000 0.000
iAPBS: SolventForces: 16 0.000 0.000 0.000
iAPBS: SolventForces: 17 0.000 0.000 0.000
iAPBS: SolventForces: 18 0.000 0.000 0.000
iAPBS: SolventForces: 19 0.000 0.000 0.000
iAPBS: SolventForces: 20 0.000 0.000 0.000
iAPBS: SolventForces: 21 0.000 0.000 0.000
iAPBS: SolventForces: 22 0.000 0.000 0.000
iAPBS: VacuumForces: 1 0.000 0.000 0.000
iAPBS: VacuumForces: 2 0.000 0.000 0.000
iAPBS: VacuumForces: 3 0.000 0.000 0.000
iAPBS: VacuumForces: 4 0.000 0.000 0.000
iAPBS: VacuumForces: 5 0.000 0.000 0.000
iAPBS: VacuumForces: 6 0.000 0.000 0.000
iAPBS: VacuumForces: 7 0.000 0.000 0.000
iAPBS: VacuumForces: 8 0.000 0.000 0.000
iAPBS: VacuumForces: 9 0.000 0.000 0.000
iAPBS: VacuumForces: 10 0.000 0.000 0.000
iAPBS: VacuumForces: 11 0.000 0.000 0.000
iAPBS: VacuumForces: 12 0.000 0.000 0.000
iAPBS: VacuumForces: 13 0.000 0.000 0.000
iAPBS: VacuumForces: 14 0.000 0.000 0.000
iAPBS: VacuumForces: 15 0.000 0.000 0.000
iAPBS: VacuumForces: 16 0.000 0.000 0.000
iAPBS: VacuumForces: 17 0.000 0.000 0.000
iAPBS: VacuumForces: 18 0.000 0.000 0.000
iAPBS: VacuumForces: 19 0.000 0.000 0.000
iAPBS: VacuumForces: 20 0.000 0.000 0.000
iAPBS: VacuumForces: 21 0.000 0.000 0.000
iAPBS: VacuumForces: 22 0.000 0.000 0.000
iAPBS: SolvForces: 1 0.000 0.000 0.000
iAPBS: SolvForces: 2 0.000 0.000 0.000
iAPBS: SolvForces: 3 0.000 0.000 0.000
iAPBS: SolvForces: 4 0.000 0.000 0.000
iAPBS: SolvForces: 5 0.000 0.000 0.000
iAPBS: SolvForces: 6 0.000 0.000 0.000
iAPBS: SolvForces: 7 0.000 0.000 0.000
iAPBS: SolvForces: 8 0.000 0.000 0.000
iAPBS: SolvForces: 9 0.000 0.000 0.000
iAPBS: SolvForces: 10 0.000 0.000 0.000
iAPBS: SolvForces: 11 0.000 0.000 0.000
iAPBS: SolvForces: 12 0.000 0.000 0.000
iAPBS: SolvForces: 13 0.000 0.000 0.000
iAPBS: SolvForces: 14 0.000 0.000 0.000
iAPBS: SolvForces: 15 0.000 0.000 0.000
iAPBS: SolvForces: 16 0.000 0.000 0.000
iAPBS: SolvForces: 17 0.000 0.000 0.000
iAPBS: SolvForces: 18 0.000 0.000 0.000
iAPBS: SolvForces: 19 0.000 0.000 0.000
iAPBS: SolvForces: 20 0.000 0.000 0.000
iAPBS: SolvForces: 21 0.000 0.000 0.000
iAPBS: SolvForces: 22 0.000 0.000 0.000
iAPBS: qfForces: 1 0.000 0.000 0.000
iAPBS: qfForces: 2 0.000 0.000 0.000
iAPBS: qfForces: 3 0.000 0.000 0.000
iAPBS: qfForces: 4 0.000 0.000 0.000
iAPBS: qfForces: 5 0.000 0.000 0.000
iAPBS: qfForces: 6 0.000 0.000 0.000
iAPBS: qfForces: 7 0.000 0.000 0.000
iAPBS: qfForces: 8 0.000 0.000 0.000
iAPBS: qfForces: 9 0.000 0.000 0.000
iAPBS: qfForces: 10 0.000 0.000 0.000
iAPBS: qfForces: 11 0.000 0.000 0.000
iAPBS: qfForces: 12 0.000 0.000 0.000
iAPBS: qfForces: 13 0.000 0.000 0.000
iAPBS: qfForces: 14 0.000 0.000 0.000
iAPBS: qfForces: 15 0.000 0.000 0.000
iAPBS: qfForces: 16 0.000 0.000 0.000
iAPBS: qfForces: 17 0.000 0.000 0.000
iAPBS: qfForces: 18 0.000 0.000 0.000
iAPBS: qfForces: 19 0.000 0.000 0.000
iAPBS: qfForces: 20 0.000 0.000 0.000
iAPBS: qfForces: 21 0.000 0.000 0.000
iAPBS: qfForces: 22 0.000 0.000 0.000
iAPBS: ibForces: 1 0.000 0.000 0.000
iAPBS: ibForces: 2 0.000 0.000 0.000
iAPBS: ibForces: 3 0.000 0.000 0.000
iAPBS: ibForces: 4 0.000 0.000 0.000
iAPBS: ibForces: 5 0.000 0.000 0.000
iAPBS: ibForces: 6 0.000 0.000 0.000
iAPBS: ibForces: 7 0.000 0.000 0.000
iAPBS: ibForces: 8 0.000 0.000 0.000
iAPBS: ibForces: 9 0.000 0.000 0.000
iAPBS: ibForces: 10 0.000 0.000 0.000
iAPBS: ibForces: 11 0.000 0.000 0.000
iAPBS: ibForces: 12 0.000 0.000 0.000
iAPBS: ibForces: 13 0.000 0.000 0.000
iAPBS: ibForces: 14 0.000 0.000 0.000
iAPBS: ibForces: 15 0.000 0.000 0.000
iAPBS: ibForces: 16 0.000 0.000 0.000
iAPBS: ibForces: 17 0.000 0.000 0.000
iAPBS: ibForces: 18 0.000 0.000 0.000
iAPBS: ibForces: 19 0.000 0.000 0.000
iAPBS: ibForces: 20 0.000 0.000 0.000
iAPBS: ibForces: 21 0.000 0.000 0.000
iAPBS: ibForces: 22 0.000 0.000 0.000
iAPBS: npForces: 1 0.000 0.000 0.000
iAPBS: npForces: 2 0.000 0.000 0.000
iAPBS: npForces: 3 0.000 0.000 0.000
iAPBS: npForces: 4 0.000 0.000 0.000
iAPBS: npForces: 5 0.000 0.000 0.000
iAPBS: npForces: 6 0.000 0.000 0.000
iAPBS: npForces: 7 0.000 0.000 0.000
iAPBS: npForces: 8 0.000 0.000 0.000
iAPBS: npForces: 9 0.000 0.000 0.000
iAPBS: npForces: 10 0.000 0.000 0.000
iAPBS: npForces: 11 0.000 0.000 0.000
iAPBS: npForces: 12 0.000 0.000 0.000
iAPBS: npForces: 13 0.000 0.000 0.000
iAPBS: npForces: 14 0.000 0.000 0.000
iAPBS: npForces: 15 0.000 0.000 0.000
iAPBS: npForces: 16 0.000 0.000 0.000
iAPBS: npForces: 17 0.000 0.000 0.000
iAPBS: npForces: 18 0.000 0.000 0.000
iAPBS: npForces: 19 0.000 0.000 0.000
iAPBS: npForces: 20 0.000 0.000 0.000
iAPBS: npForces: 21 0.000 0.000 0.000
iAPBS: npForces: 22 0.000 0.000 0.000
iAPBS: dbForces: 1 0.000 0.000 0.000
iAPBS: dbForces: 2 0.000 0.000 0.000
iAPBS: dbForces: 3 0.000 0.000 0.000
iAPBS: dbForces: 4 0.000 0.000 0.000
iAPBS: dbForces: 5 0.000 0.000 0.000
iAPBS: dbForces: 6 0.000 0.000 0.000
iAPBS: dbForces: 7 0.000 0.000 0.000
iAPBS: dbForces: 8 0.000 0.000 0.000
iAPBS: dbForces: 9 0.000 0.000 0.000
iAPBS: dbForces: 10 0.000 0.000 0.000
iAPBS: dbForces: 11 0.000 0.000 0.000
iAPBS: dbForces: 12 0.000 0.000 0.000
iAPBS: dbForces: 13 0.000 0.000 0.000
iAPBS: dbForces: 14 0.000 0.000 0.000
iAPBS: dbForces: 15 0.000 0.000 0.000
iAPBS: dbForces: 16 0.000 0.000 0.000
iAPBS: dbForces: 17 0.000 0.000 0.000
iAPBS: dbForces: 18 0.000 0.000 0.000
iAPBS: dbForces: 19 0.000 0.000 0.000
iAPBS: dbForces: 20 0.000 0.000 0.000
iAPBS: dbForces: 21 0.000 0.000 0.000
iAPBS: dbForces: 22 0.000 0.000 0.000
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.8500E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -13.5448
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.8500E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -13.5448
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.02% of Total)
| PB Nonbond 2.13 (100.0% of Nonbo)
| Nonbond force 2.13 (100.0% of Force)
| Force time 2.13 (100.0% of Runmd)
| Runmd Time 2.13 (99.87% of Total)
| Other 0.00 ( 0.10% of Total)
| Total time 2.14 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 22:02:40.741 on 09/24/2007
| Setup done at 22:02:40.743 on 09/24/2007
| Run done at 22:02:42.878 on 09/24/2007
| wallclock() was called 22 times

22
contrib/iapbs/modules/Amber/test/Solvation/debug/solvation.in Normal file
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APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=9,
apbs_print=1,
grid=0.5, 0.5, 0.5,
calc_type=0,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
&end

344
contrib/iapbs/modules/Amber/test/Solvation/debug/solvation.log Normal file
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debug: Input string:
read
mol pqr ion.pqr
end
elec name elec
mg-manual
dime 33 33 33
grid 0.500 0.500 0.500
nlev 4
gcent mol 1
pdie 1.000
sdie 78.540
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl mdh
srfm smol
calcenergy total
calcforce no
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
quit
Parsed input string.
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.500 x 0.500 x 0.500
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (4.112, 4.824, -0.621)
Multigrid levels: 4
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
----------------------------------------
CALCULATION #2 (npolar): APOLAR
energyAPOL: 41.489065
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148906464712E+01 kJ/mol
print APOL force 1 (npolar) 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 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sasa 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sasa 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sav 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sasa 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sav 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sasa 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sav 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sasa 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sav 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sasa 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sav 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sasa 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sav 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sasa 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sav 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sasa 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sav 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sasa 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sav 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sasa 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sav 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sasa 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sav 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sasa 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sav 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sasa 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sav 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sasa 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sav 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sasa 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sav 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sasa 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sav 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sasa 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sav 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sasa 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
sav 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
tot all 1.010028716361E+01 2.172761646898E+01 2.668403298113E+00
----------------------------------------
Final memory usage: 8.692 MB total, 8.902 MB high water
debug: Input string:
read
mol pqr ion.pqr
end
elec name elec
mg-manual
dime 33 33 33
grid 0.500 0.500 0.500
nlev 4
gcent mol 1
pdie 1.000
sdie 1.000
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
mol 1
chgm spl2
lpbe
bcfl mdh
srfm smol
calcenergy total
calcforce no
end
apolar name npolar
bconc 0.0
press 0.0
dpos 0.2
mol 1
srfm sacc
grid 0.2 0.2 0.2
gamma 0.105
srad 1.400
swin 0.300
temp 298.150
sdens 10.000
calcenergy total
calcforce comps
end
quit
Parsed input string.
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
Setting up problem...
Using cubic spline charge discretization.
Grid dimensions: 33 x 33 x 33
Grid spacings: 0.500 x 0.500 x 0.500
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (4.112, 4.824, -0.621)
Multigrid levels: 4
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
----------------------------------------
CALCULATION #2 (npolar): APOLAR
energyAPOL: 41.489065
print APOL energy 1 (npolar) end
Global net APOL energy = 4.148906464712E+01 kJ/mol
print APOL force 1 (npolar) 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 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00
sasa 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00
sasa 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sav 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 2 -1.881066742799E+01 -7.524266971198E-01 1.926212344627E+01
sasa 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sav 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 3 -1.941260878569E+01 -1.805824073087E+00 -1.775727005203E+01
sasa 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sav 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00
sasa 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sav 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00
sasa 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sav 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00
sasa 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sav 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00
sasa 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sav 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01
sasa 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sav 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 10 2.410412977298E+01 -1.086661588126E+01 -2.133808209412E+01
sasa 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sav 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01
sasa 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sav 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00
sasa 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sav 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 13 1.866018208857E+01 -1.610193131836E+01 -1.143688579622E+01
sasa 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sav 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01
sasa 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sav 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00
sasa 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sav 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00
sasa 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sav 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
sasa 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sav 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 18 3.951496684096E+00 4.307131385664E+01 3.951496684096E-01
sasa 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sav 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 19 -1.626793959208E+01 2.468239110523E+01 0.000000000000E+00
sasa 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sav 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01
sasa 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
sav 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
wca 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
tot 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01
tot all 1.010028716361E+01 2.172761646898E+01 2.668403298113E+00
----------------------------------------
Final memory usage: 17.205 MB total, 17.415 MB high water

400
contrib/iapbs/modules/Amber/test/Solvation/debug/solvation.out Normal file
View File

@@ -0,0 +1,400 @@
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 09/24/2007 at 22:04:50
[-O]verwriting output
File Assignments:
| MDIN: solvation.in
| MDOUT: Ba
|INPCRD: 2ala.prmcrd
| PARM: 2ala.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=9,
apbs_print=1,
grid=0.5, 0.5, 0.5,
calc_type=0,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 10/18/06 Time = 21:21:36
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 42 MPHIA = 18
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 18 NUMBND = 8
NUMANG = 16 NPTRA = 16 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 1592
| Hollerith 137
| Integer 21004
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 95 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 6, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
iAPBS: Initializing APBS interface
iAPBS: Reading radii definition from pqr filename: 2ala.pqr
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting recalculating dime during caclulations.
iAPBS: Grid values:
fglen: 13.801 18.154 10.192
cglen: 13.801 18.154 10.192
dime: 33 33 33
grid: 0.500 0.500 0.500
Required memory (in MB): 6.854
APBS calculation parameters:
Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Smoothed molecular surface definition.
Using cubic B-spline discretization
Grid dimension: 33 33 33
Coarse grid lengths: 13.801 18.154 10.192
Fine grid lengths: 13.801 18.154 10.192
Grid spacings: 0.500 0.500 0.500
Solute dielectric (pdie): 1.000
Solvent dielectric (sdie): 78.540
Temperature: 298.150
Surface sphere density (sdens): 10.000
Surface tension: 0.105
radiopt is set to 3
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
iAPBS: unpacked coordinates, charge and radius:
1 2.000 1.000 0.000 0.112 1.487
2 2.000 2.090 0.000 -0.366 1.908
3 1.486 2.454 0.890 0.112 1.487
4 1.486 2.454 -0.890 0.112 1.487
5 3.427 2.641 0.000 0.597 1.908
6 4.391 1.877 0.000 -0.568 1.661
7 3.555 3.970 0.000 -0.416 1.824
8 2.733 4.556 0.000 0.272 0.600
9 4.853 4.614 0.000 0.034 1.908
10 5.408 4.316 0.890 0.082 1.387
11 5.661 4.221 -1.232 -0.182 1.908
12 5.123 4.521 -2.131 0.060 1.487
13 6.630 4.719 -1.206 0.060 1.487
14 5.809 3.141 -1.241 0.060 1.487
15 4.713 6.129 0.000 0.597 1.908
16 3.601 6.653 0.000 -0.568 1.661
17 5.846 6.835 0.000 -0.416 1.824
18 6.737 6.359 0.000 0.272 0.600
19 5.846 8.284 0.000 -0.149 1.908
20 4.819 8.648 0.000 0.098 1.387
21 6.360 8.648 0.890 0.098 1.387
22 6.360 8.648 -0.890 0.098 1.387
iAPBS: Calling apbsdrv
iAPBS: apbs return code: 0
iAPBS: apbs return code: 0
iAPBS: TotalForces: 1 4.108 0.761 -0.017
iAPBS: TotalForces: 2 6.437 8.400 0.055
iAPBS: TotalForces: 3 0.126 -1.054 -1.019
iAPBS: TotalForces: 4 0.162 -1.035 0.979
iAPBS: TotalForces: 5 -10.816 -5.205 3.291
iAPBS: TotalForces: 6 -15.856 -9.593 9.277
iAPBS: TotalForces: 7 -1.998 -18.943 -5.755
iAPBS: TotalForces: 8 1.173 1.094 -0.176
iAPBS: TotalForces: 9 8.610 9.436 1.432
iAPBS: TotalForces: 10 -0.417 -0.207 1.012
iAPBS: TotalForces: 11 0.958 -4.145 -7.140
iAPBS: TotalForces: 12 0.424 -0.661 -1.502
iAPBS: TotalForces: 13 1.974 -4.806 -3.120
iAPBS: TotalForces: 14 9.767 6.261 -7.979
iAPBS: TotalForces: 15 -1.239 0.475 7.502
iAPBS: TotalForces: 16 -5.177 -1.051 -0.431
iAPBS: TotalForces: 17 -1.541 8.188 3.810
iAPBS: TotalForces: 18 -3.350 -2.477 -0.165
iAPBS: TotalForces: 19 6.599 4.841 -0.004
iAPBS: TotalForces: 20 0.937 6.805 -0.022
iAPBS: TotalForces: 21 -0.437 1.472 0.515
iAPBS: TotalForces: 22 -0.447 1.444 -0.543
iAPBS: SolventForces: 1 0.000 0.000 0.000
iAPBS: SolventForces: 2 0.000 0.000 0.000
iAPBS: SolventForces: 3 0.000 0.000 0.000
iAPBS: SolventForces: 4 0.000 0.000 0.000
iAPBS: SolventForces: 5 0.000 0.000 0.000
iAPBS: SolventForces: 6 0.000 0.000 0.000
iAPBS: SolventForces: 7 0.000 0.000 0.000
iAPBS: SolventForces: 8 0.000 0.000 0.000
iAPBS: SolventForces: 9 0.000 0.000 0.000
iAPBS: SolventForces: 10 0.000 0.000 0.000
iAPBS: SolventForces: 11 0.000 0.000 0.000
iAPBS: SolventForces: 12 0.000 0.000 0.000
iAPBS: SolventForces: 13 0.000 0.000 0.000
iAPBS: SolventForces: 14 0.000 0.000 0.000
iAPBS: SolventForces: 15 0.000 0.000 0.000
iAPBS: SolventForces: 16 0.000 0.000 0.000
iAPBS: SolventForces: 17 0.000 0.000 0.000
iAPBS: SolventForces: 18 0.000 0.000 0.000
iAPBS: SolventForces: 19 0.000 0.000 0.000
iAPBS: SolventForces: 20 0.000 0.000 0.000
iAPBS: SolventForces: 21 0.000 0.000 0.000
iAPBS: SolventForces: 22 0.000 0.000 0.000
iAPBS: VacuumForces: 1 0.000 0.000 0.000
iAPBS: VacuumForces: 2 0.000 0.000 0.000
iAPBS: VacuumForces: 3 0.000 0.000 0.000
iAPBS: VacuumForces: 4 0.000 0.000 0.000
iAPBS: VacuumForces: 5 0.000 0.000 0.000
iAPBS: VacuumForces: 6 0.000 0.000 0.000
iAPBS: VacuumForces: 7 0.000 0.000 0.000
iAPBS: VacuumForces: 8 0.000 0.000 0.000
iAPBS: VacuumForces: 9 0.000 0.000 0.000
iAPBS: VacuumForces: 10 0.000 0.000 0.000
iAPBS: VacuumForces: 11 0.000 0.000 0.000
iAPBS: VacuumForces: 12 0.000 0.000 0.000
iAPBS: VacuumForces: 13 0.000 0.000 0.000
iAPBS: VacuumForces: 14 0.000 0.000 0.000
iAPBS: VacuumForces: 15 0.000 0.000 0.000
iAPBS: VacuumForces: 16 0.000 0.000 0.000
iAPBS: VacuumForces: 17 0.000 0.000 0.000
iAPBS: VacuumForces: 18 0.000 0.000 0.000
iAPBS: VacuumForces: 19 0.000 0.000 0.000
iAPBS: VacuumForces: 20 0.000 0.000 0.000
iAPBS: VacuumForces: 21 0.000 0.000 0.000
iAPBS: VacuumForces: 22 0.000 0.000 0.000
iAPBS: SolvForces: 1 0.000 0.000 0.000
iAPBS: SolvForces: 2 0.000 0.000 0.000
iAPBS: SolvForces: 3 0.000 0.000 0.000
iAPBS: SolvForces: 4 0.000 0.000 0.000
iAPBS: SolvForces: 5 0.000 0.000 0.000
iAPBS: SolvForces: 6 0.000 0.000 0.000
iAPBS: SolvForces: 7 0.000 0.000 0.000
iAPBS: SolvForces: 8 0.000 0.000 0.000
iAPBS: SolvForces: 9 0.000 0.000 0.000
iAPBS: SolvForces: 10 0.000 0.000 0.000
iAPBS: SolvForces: 11 0.000 0.000 0.000
iAPBS: SolvForces: 12 0.000 0.000 0.000
iAPBS: SolvForces: 13 0.000 0.000 0.000
iAPBS: SolvForces: 14 0.000 0.000 0.000
iAPBS: SolvForces: 15 0.000 0.000 0.000
iAPBS: SolvForces: 16 0.000 0.000 0.000
iAPBS: SolvForces: 17 0.000 0.000 0.000
iAPBS: SolvForces: 18 0.000 0.000 0.000
iAPBS: SolvForces: 19 0.000 0.000 0.000
iAPBS: SolvForces: 20 0.000 0.000 0.000
iAPBS: SolvForces: 21 0.000 0.000 0.000
iAPBS: SolvForces: 22 0.000 0.000 0.000
iAPBS: qfForces: 1 0.000 0.000 0.000
iAPBS: qfForces: 2 0.000 0.000 0.000
iAPBS: qfForces: 3 0.000 0.000 0.000
iAPBS: qfForces: 4 0.000 0.000 0.000
iAPBS: qfForces: 5 0.000 0.000 0.000
iAPBS: qfForces: 6 0.000 0.000 0.000
iAPBS: qfForces: 7 0.000 0.000 0.000
iAPBS: qfForces: 8 0.000 0.000 0.000
iAPBS: qfForces: 9 0.000 0.000 0.000
iAPBS: qfForces: 10 0.000 0.000 0.000
iAPBS: qfForces: 11 0.000 0.000 0.000
iAPBS: qfForces: 12 0.000 0.000 0.000
iAPBS: qfForces: 13 0.000 0.000 0.000
iAPBS: qfForces: 14 0.000 0.000 0.000
iAPBS: qfForces: 15 0.000 0.000 0.000
iAPBS: qfForces: 16 0.000 0.000 0.000
iAPBS: qfForces: 17 0.000 0.000 0.000
iAPBS: qfForces: 18 0.000 0.000 0.000
iAPBS: qfForces: 19 0.000 0.000 0.000
iAPBS: qfForces: 20 0.000 0.000 0.000
iAPBS: qfForces: 21 0.000 0.000 0.000
iAPBS: qfForces: 22 0.000 0.000 0.000
iAPBS: ibForces: 1 0.000 0.000 0.000
iAPBS: ibForces: 2 0.000 0.000 0.000
iAPBS: ibForces: 3 0.000 0.000 0.000
iAPBS: ibForces: 4 0.000 0.000 0.000
iAPBS: ibForces: 5 0.000 0.000 0.000
iAPBS: ibForces: 6 0.000 0.000 0.000
iAPBS: ibForces: 7 0.000 0.000 0.000
iAPBS: ibForces: 8 0.000 0.000 0.000
iAPBS: ibForces: 9 0.000 0.000 0.000
iAPBS: ibForces: 10 0.000 0.000 0.000
iAPBS: ibForces: 11 0.000 0.000 0.000
iAPBS: ibForces: 12 0.000 0.000 0.000
iAPBS: ibForces: 13 0.000 0.000 0.000
iAPBS: ibForces: 14 0.000 0.000 0.000
iAPBS: ibForces: 15 0.000 0.000 0.000
iAPBS: ibForces: 16 0.000 0.000 0.000
iAPBS: ibForces: 17 0.000 0.000 0.000
iAPBS: ibForces: 18 0.000 0.000 0.000
iAPBS: ibForces: 19 0.000 0.000 0.000
iAPBS: ibForces: 20 0.000 0.000 0.000
iAPBS: ibForces: 21 0.000 0.000 0.000
iAPBS: ibForces: 22 0.000 0.000 0.000
iAPBS: npForces: 1 0.000 0.000 0.000
iAPBS: npForces: 2 0.000 0.000 0.000
iAPBS: npForces: 3 0.000 0.000 0.000
iAPBS: npForces: 4 0.000 0.000 0.000
iAPBS: npForces: 5 0.000 0.000 0.000
iAPBS: npForces: 6 0.000 0.000 0.000
iAPBS: npForces: 7 0.000 0.000 0.000
iAPBS: npForces: 8 0.000 0.000 0.000
iAPBS: npForces: 9 0.000 0.000 0.000
iAPBS: npForces: 10 0.000 0.000 0.000
iAPBS: npForces: 11 0.000 0.000 0.000
iAPBS: npForces: 12 0.000 0.000 0.000
iAPBS: npForces: 13 0.000 0.000 0.000
iAPBS: npForces: 14 0.000 0.000 0.000
iAPBS: npForces: 15 0.000 0.000 0.000
iAPBS: npForces: 16 0.000 0.000 0.000
iAPBS: npForces: 17 0.000 0.000 0.000
iAPBS: npForces: 18 0.000 0.000 0.000
iAPBS: npForces: 19 0.000 0.000 0.000
iAPBS: npForces: 20 0.000 0.000 0.000
iAPBS: npForces: 21 0.000 0.000 0.000
iAPBS: npForces: 22 0.000 0.000 0.000
iAPBS: dbForces: 1 0.000 0.000 0.000
iAPBS: dbForces: 2 0.000 0.000 0.000
iAPBS: dbForces: 3 0.000 0.000 0.000
iAPBS: dbForces: 4 0.000 0.000 0.000
iAPBS: dbForces: 5 0.000 0.000 0.000
iAPBS: dbForces: 6 0.000 0.000 0.000
iAPBS: dbForces: 7 0.000 0.000 0.000
iAPBS: dbForces: 8 0.000 0.000 0.000
iAPBS: dbForces: 9 0.000 0.000 0.000
iAPBS: dbForces: 10 0.000 0.000 0.000
iAPBS: dbForces: 11 0.000 0.000 0.000
iAPBS: dbForces: 12 0.000 0.000 0.000
iAPBS: dbForces: 13 0.000 0.000 0.000
iAPBS: dbForces: 14 0.000 0.000 0.000
iAPBS: dbForces: 15 0.000 0.000 0.000
iAPBS: dbForces: 16 0.000 0.000 0.000
iAPBS: dbForces: 17 0.000 0.000 0.000
iAPBS: dbForces: 18 0.000 0.000 0.000
iAPBS: dbForces: 19 0.000 0.000 0.000
iAPBS: dbForces: 20 0.000 0.000 0.000
iAPBS: dbForces: 21 0.000 0.000 0.000
iAPBS: dbForces: 22 0.000 0.000 0.000
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.9290E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -14.3348
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.9290E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -14.3348
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.06% of Total)
| PB Nonbond 0.88 (100.0% of Nonbo)
| Nonbond force 0.88 (100.0% of Force)
| Bond/Angle/Dihedral 0.00 ( 0.01% of Force)
| Force time 0.88 (100.0% of Runmd)
| Runmd Time 0.88 (99.69% of Total)
| Other 0.00 ( 0.25% of Total)
| Total time 0.88 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 22:04:50.491 on 09/24/2007
| Setup done at 22:04:50.494 on 09/24/2007
| Run done at 22:04:51.373 on 09/24/2007
| wallclock() was called 22 times

23
contrib/iapbs/modules/Amber/test/Solvation/maps-read.in Normal file
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APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=0,
apbs_print=1,
grid=0.5, 0.5, 0.5,
calc_type=1,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
rchg=1, rkappa=1, rdiel=1,
&end

23
contrib/iapbs/modules/Amber/test/Solvation/maps.in Normal file
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APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=0,
apbs_print=1,
grid=0.5, 0.5, 0.5,
calc_type=1,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
wpot=1, wchg=1, wkappa=1, wdiel=1,
&end

19
contrib/iapbs/modules/Amber/test/Solvation/notes.txt Normal file
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= This is a solvation test for iAPBS =
Last Modified: 09/24/07 16:10:54 (rok)
== Notes ==
2ala.pqr: pdb2pqr could not assing ACE's Hs and NME's Hs, too info
from amber
debug directory: contains run with print and debug options jacked up
APBS directory: files for apbs run
PBSA directory: files for Amber/pbsa run
== Run ==
./Run.apbs.solv

24
contrib/iapbs/modules/Amber/test/Solvation/solvation-auto.in Normal file
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APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=0,
apbs_print=1,
fglen= 13.801, 18.154, 10.192,
cglen= 13.801, 18.154 10.192,
dime= 33, 33, 33,
calc_type=1,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
&end

191
contrib/iapbs/modules/Amber/test/Solvation/solvation-auto.out.save Normal file
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-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 05/28/2008 at 14:21:09
[-O]verwriting output
File Assignments:
| MDIN: solvation-auto.in
| MDOUT: solvation-auto.out
|INPCRD: 2ala.prmcrd
| PARM: 2ala.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=0,
apbs_print=1,
fglen= 13.801, 18.154, 10.192,
cglen= 13.801, 18.154 10.192,
dime= 33, 33, 33,
calc_type=1,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 10/18/06 Time = 21:21:36
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 42 MPHIA = 18
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 18 NUMBND = 8
NUMANG = 16 NPTRA = 16 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 1592
| Hollerith 137
| Integer 21004
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 95 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 6, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
iAPBS: Initializing APBS interface
iAPBS: Reading radii definition from pqr filename: 2ala.pqr
APBS calculation parameters:
Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Smoothed molecular surface definition
Using cubic B-spline discretization
Grid dimension: 33 33 33
Coarse grid lengths: 13.801 18.154 10.192 A
Fine grid lengths: 13.801 18.154 10.192 A
Solute dielectric (pdie): 1.000
Solvent dielectric (sdie): 78.540
Temperature: 298.150 K
Surface sphere density (sdens): 10.000 grid points/A^2
Surface tension: 0.105 kJ/mol/A
Using radii information form PQR file
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.8500E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -13.5448
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.8500E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -13.5448
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.03% of Total)
| PB Nonbond 2.05 (100.0% of Nonbo)
| Nonbond force 2.05 (100.0% of Force)
| Bond/Angle/Dihedral 0.00 ( 0.01% of Force)
| Force time 2.05 (100.0% of Runmd)
| Runmd Time 2.05 (99.84% of Total)
| Other 0.00 ( 0.13% of Total)
| Total time 2.05 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 14:21:09.353 on 05/28/2008
| Setup done at 14:21:09.356 on 05/28/2008
| Run done at 14:21:11.405 on 05/28/2008
| wallclock() was called 22 times

22
contrib/iapbs/modules/Amber/test/Solvation/solvation.in Normal file
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APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=0,
apbs_print=1,
grid=0.5, 0.5, 0.5,
calc_type=1,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcenergy=1, calcforce=0, calcnpenergy=1, calcnpforce=0,
&end

202
contrib/iapbs/modules/Amber/test/Solvation/solvation.out.save Normal file
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-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 05/28/2008 at 14:21:08
[-O]verwriting output
File Assignments:
| MDIN: solvation.in
| MDOUT: solvation.out
|INPCRD: 2ala.prmcrd
| PARM: 2ala.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
APBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug=0,
apbs_print=1,
grid=0.5, 0.5, 0.5,
calc_type=0,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=78.54,
srad = 1.4,
radiopt=3, pqr='2ala.pqr',
calcforce=0, calcnpenergy=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 10/18/06 Time = 21:21:36
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 42 MPHIA = 18
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 18 NUMBND = 8
NUMANG = 16 NPTRA = 16 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 1592
| Hollerith 137
| Integer 21004
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 95 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 6, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
iAPBS: Initializing APBS interface
iAPBS: Reading radii definition from pqr filename: 2ala.pqr
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting dime re-calculation on the fly
iAPBS: Grid values:
iAPBS: fglen: 13.801 18.154 10.192
iAPBS: cglen: 13.801 18.154 10.192
iAPBS: dime: 33 33 33
iAPBS: grid: 0.500 0.500 0.500
iAPBS: Required memory (in MB): 6.854
APBS calculation parameters:
Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Smoothed molecular surface definition
Using cubic B-spline discretization
Grid dimension: 33 33 33
Coarse grid lengths: 13.801 18.154 10.192 A
Fine grid lengths: 13.801 18.154 10.192 A
Grid spacings: 0.500 0.500 0.500 A
Solute dielectric (pdie): 1.000
Solvent dielectric (sdie): 78.540
Temperature: 298.150 K
Surface sphere density (sdens): 10.000 grid points/A^2
Surface tension: 0.105 kJ/mol/A
Using radii information form PQR file
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.9290E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -14.3348
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.9290E+01 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = -14.3348
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 9.9161
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.13% of Total)
| Calc gb off-diag 0.00 (99.80% of Gen B)
| Other 0.00 ( 0.20% of Gen B)
| Gen Born time 0.00 ( 0.27% of Nonbo)
| PB Nonbond 0.92 (99.73% of Nonbo)
| Nonbond force 0.93 (98.67% of Force)
| Bond/Angle/Dihedral 0.00 ( 0.01% of Force)
| Other 0.01 ( 1.31% of Force)
| Force time 0.94 (100.0% of Runmd)
| Runmd Time 0.94 (85.91% of Total)
| Other 0.15 (13.96% of Total)
| Total time 1.09 (98.81% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 14:21:08.173 on 05/28/2008
| Setup done at 14:21:08.342 on 05/28/2008
| Run done at 14:21:09.284 on 05/28/2008
| wallclock() was called 22 times

24
contrib/iapbs/modules/Amber/test/Visualization/2ala.pdb Normal file
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REMARK ACE
ATOM 1 1HH3 ACE 1 2.000 1.000 0.000
ATOM 2 CH3 ACE 1 2.000 2.090 0.000
ATOM 3 2HH3 ACE 1 1.486 2.454 0.890
ATOM 4 3HH3 ACE 1 1.486 2.454 -0.890
ATOM 5 C ACE 1 3.427 2.641 0.000
ATOM 6 O ACE 1 4.391 1.877 0.000
ATOM 7 N ALA 2 3.555 3.970 0.000
ATOM 8 H ALA 2 2.733 4.556 0.000
ATOM 9 CA ALA 2 4.853 4.614 0.000
ATOM 10 HA ALA 2 5.408 4.316 0.890
ATOM 11 CB ALA 2 5.661 4.221 -1.232
ATOM 12 1HB ALA 2 5.123 4.521 -2.131
ATOM 13 2HB ALA 2 6.630 4.719 -1.206
ATOM 14 3HB ALA 2 5.809 3.141 -1.241
ATOM 15 C ALA 2 4.713 6.129 0.000
ATOM 16 O ALA 2 3.601 6.653 0.000
ATOM 17 N NME 3 5.846 6.835 0.000
ATOM 18 H NME 3 6.737 6.359 0.000
ATOM 19 CH3 NME 3 5.846 8.284 0.000
ATOM 20 1HH3 NME 3 4.819 8.648 0.000
ATOM 21 2HH3 NME 3 6.360 8.648 0.890
ATOM 22 3HH3 NME 3 6.360 8.648 -0.890
END

43
contrib/iapbs/modules/Amber/test/Visualization/2ala.pqr Normal file
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REMARK 1 PQR file generated by PDB2PQR (Version 1.2.1)
REMARK 1
REMARK 1 Forcefield Used: amber
REMARK 1
REMARK 5
REMARK 5 WARNING: PDB2PQR was unable to assign charges
REMARK 5 to the following atoms (omitted below):
REMARK 5 1 1HH3 in ACE 1
REMARK 5 3 2HH3 in ACE 1
REMARK 5 4 3HH3 in ACE 1
REMARK 5 20 1HH3 in NME 3
REMARK 5 21 2HH3 in NME 3
REMARK 5 22 3HH3 in NME 3
REMARK 5
REMARK 5 WARNING: Non-integral net charges were found in
REMARK 5 the following residues:
REMARK 5 ACE A 1 - Residue Charge: -0.3369
REMARK 5 NME A 3 - Residue Charge: -0.2928
REMARK 5
REMARK 6 Total charge on this protein: -0.6297 e
REMARK 6
ATOM 1 1HH3 ACE 1 2.000 1.000 0.000 0.1123 1.487
ATOM 2 CH3 ACE 1 2.000 2.090 0.000 -0.3662 1.9080
ATOM 3 2HH3 ACE 1 1.486 2.454 0.890 0.1123 1.487
ATOM 4 3HH3 ACE 1 1.486 2.454 -0.890 0.1123 1.487
ATOM 5 C ACE 1 3.427 2.641 0.000 0.5972 1.9080
ATOM 6 O ACE 1 4.391 1.877 0.000 -0.5679 1.6612
ATOM 7 N ALA 2 3.555 3.970 0.000 -0.4157 1.8240
ATOM 8 H ALA 2 2.733 4.556 0.000 0.2719 0.6000
ATOM 9 CA ALA 2 4.853 4.614 0.000 0.0337 1.9080
ATOM 10 HA ALA 2 5.408 4.316 0.890 0.0823 1.3870
ATOM 11 CB ALA 2 5.661 4.221 -1.232 -0.1825 1.9080
ATOM 12 HB1 ALA 2 5.123 4.521 -2.131 0.0603 1.4870
ATOM 13 HB2 ALA 2 6.630 4.719 -1.206 0.0603 1.4870
ATOM 14 HB3 ALA 2 5.809 3.141 -1.241 0.0603 1.4870
ATOM 15 C ALA 2 4.713 6.129 0.000 0.5973 1.9080
ATOM 16 O ALA 2 3.601 6.653 0.000 -0.5679 1.6612
ATOM 17 N NME 3 5.846 6.835 0.000 -0.4157 1.8240
ATOM 18 H NME 3 6.737 6.359 0.000 0.2719 0.6000
ATOM 19 CH3 NME 3 5.846 8.284 0.000 -0.1490 1.9080
ATOM 20 1HH3 NME 3 4.819 8.648 0.000 0.0976 1.387
ATOM 21 2HH3 NME 3 6.360 8.648 0.890 0.0976 1.387
ATOM 22 3HH3 NME 3 6.360 8.648 -0.890 0.0976 1.387

13
contrib/iapbs/modules/Amber/test/Visualization/2ala.prmcrd Normal file
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ACE
22
2.0000010 1.0000000 -0.0000013 2.0000010 2.0900000 0.0000001
1.4862640 2.4538490 0.8898240 1.4862590 2.4538520 -0.8898200
3.4274200 2.6407950 -0.0000030 4.3905800 1.8774060 -0.0000066
3.5553754 3.9696488 -0.0000031 2.7331200 4.5561601 -0.0000013
4.8532621 4.6139253 -0.0000043 5.4075960 4.3155388 0.8898151
5.6613044 4.2208425 -1.2321480 5.1232615 4.5213630 -2.1312016
6.6304840 4.7189354 -1.2057908 5.8085401 3.1408723 -1.2413850
4.7126759 6.1294185 0.0000014 3.6006445 6.6527027 0.0000062
5.8460533 6.8348833 0.0000025 6.7370014 6.3591620 -0.0000004
5.8460551 8.2838837 0.0000062 4.8185761 8.6477349 0.0000104
6.3597984 8.6477313 0.8898282 6.3597900 8.6477354 -0.8898188

229
contrib/iapbs/modules/Amber/test/Visualization/2ala.prmtop Normal file
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%VERSION VERSION_STAMP = V0001.000 DATE = 10/18/06 21:21:36
%FLAG TITLE
%FORMAT(20a4)
ACE
%FLAG POINTERS
%FORMAT(10I8)
22 7 12 9 25 11 42 18 0 0
99 3 9 11 18 8 16 16 7 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
HH32HH33
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
1.77849648E+00 1.77849648E+00
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 1 3 4 5 6 2 7
2 1 1 1 3 4 5 6 2 7
7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
6 7 4 3 7 3 10 4 10 7
6 3 2 1 7 3 5 4 3 2
1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 2 3 5
8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
21 27 22 23 24 25 26 27 28
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ACE ALA NME
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 7 17
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
3.10000000E+02 4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
1.52600000E+00 1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01
8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01
5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01
3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00
1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 5.30000000E-01 1.50000000E-01
5.00000000E-01 8.00000000E-01 8.50000000E-01 8.00000000E-02 1.55555556E-01
7.00000000E-02 1.00000000E-01 1.70000000E+00 2.00000000E+00 1.05000000E+01
1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00
2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
6.20665997E+04 5.94667300E+01 3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.13252061E+02 1.93248820E+00 1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
3 6 3 3 9 3 0 3 3 30
33 3 30 36 3 30 39 3 24 27
5 18 21 7 54 57 5 54 60 5
54 63 5 48 51 7
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 15 1 12 18 2 3 12 4 42
45 1 42 48 2 24 30 6 24 42
4 18 24 8 48 54 8
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
12 18 21 2 9 3 12 4 6 3
9 5 6 3 12 4 0 3 6 5
0 3 9 5 0 3 12 4 42 48
51 2 36 30 39 5 33 30 36 5
33 30 39 5 27 24 30 9 27 24
42 10 24 30 33 11 24 30 36 11
24 30 39 11 21 18 24 12 18 24
27 13 60 54 63 16 57 54 60 16
57 54 63 16 51 48 54 12 48 54
57 13 48 54 60 13 48 54 63 13
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 1 12 18 24 3 3 12
15 6 3 12 18 7 45 42 48 1
42 48 54 3 30 24 42 8 24 42
45 6 24 42 48 7 18 24 30 14
18 24 42 15
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
15 12 18 21 1 15 12 -18 21 2
12 18 24 27 3 9 3 12 15 7
9 3 -12 15 3 9 3 -12 15 9
9 3 12 18 3 6 3 12 15 7
6 3 -12 15 3 6 3 -12 15 9
6 3 12 18 3 3 12 18 21 2
0 3 12 15 7 0 3 -12 15 3
0 3 -12 15 9 0 3 12 18 3
45 42 48 51 1 45 42 -48 51 2
42 48 54 57 3 42 48 54 60 3
42 48 54 63 3 39 30 24 42 10
36 30 24 42 10 33 30 24 42 10
27 24 30 33 10 27 24 30 36 10
27 24 30 39 10 27 24 42 45 7
27 24 -42 45 9 27 24 42 48 3
24 42 48 51 2 21 18 24 27 3
21 18 24 30 3 21 18 24 42 3
18 24 30 33 10 18 24 30 36 10
18 24 30 39 10 51 48 54 57 3
51 48 54 60 3 51 48 54 63 3
12 24 -18 -21 16 42 54 -48 -51 16
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 24 2 12 18 24 30 4
12 18 -24 30 3 12 18 -24 30 5
12 18 -24 30 6 12 18 24 42 7
12 18 -24 42 8 3 12 18 24 2
45 42 48 54 2 30 24 42 45 3
30 24 42 48 11 30 24 -42 48 12
24 42 48 54 2 18 24 42 45 3
18 24 42 48 13 18 24 -42 48 14
3 18 -12 -15 15 24 48 -42 -45 15
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 3 4 5 6
7 8 9 4 5 6 7 5 6 7
6 7 8 9 10 11 15 7 8 9
8 9 10 11 12 13 14 15 16 17
9 10 11 15 10 11 12 13 14 15
16 17 18 19 11 12 13 14 15 16
17 12 13 14 15 16 17 13 14 15
14 15 15 16 17 18 19 20 21 22
17 18 19 18 19 20 21 22 19 20
21 22 20 21 22 21 22 22 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1
H1 H1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E M E M E M E 3 E E E M E M E M E
E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01

13
contrib/iapbs/modules/Amber/test/Visualization/Run.apbs.vis Normal file
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#!/bin/sh
export MCSH_HOME=/dev/null
output=vis.out
$AMBERHOME/bin/sander.APBS -O -i vis.in \
-c 2ala.prmcrd -p 2ala.prmtop -o $output
$AMBERHOME/test/dacdif $output.save $output
/bin/rm -f mdinfo restrt

18
contrib/iapbs/modules/Amber/test/Visualization/vis.in Normal file
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APBS visualization example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0
ntpr=1,
/
&apbs
apbs_debug = 100,
apbs_print=100,
calc_type = 0,
grid = 0.5, 0.5, 0.5,
srad = 0.7,
wpot = 1, wchg = 1, wsmol =1,
sp_apbs=.true.,
calcnpenergy=0, calcnpforce=0,
&end

195
contrib/iapbs/modules/Amber/test/Visualization/vis.out.save Normal file
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-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 05/28/2008 at 14:28:33
[-O]verwriting output
File Assignments:
| MDIN: vis.in
| MDOUT: vis.out
|INPCRD: 2ala.prmcrd
| PARM: 2ala.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
APBS visualization example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0
ntpr=1,
/
&apbs
apbs_debug = 0,
apbs_print=1,
calc_type = 0,
grid = 0.5, 0.5, 0.5,
srad = 0.7,
wpot = 1, wchg = 1, wsmol =1,
sp_apbs=.true.,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 10/18/06 Time = 21:21:36
NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9
NTHETH = 25 MTHETA = 11 NPHIH = 42 MPHIA = 18
NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3
NBONA = 9 NTHETA = 11 NPHIA = 18 NUMBND = 8
NUMANG = 16 NPTRA = 16 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 1592
| Hollerith 137
| Integer 21004
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 95 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 6, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
iAPBS: Initializing APBS interface
iAPBS: Using charge/radii definition from prmtop file
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting dime re-calculation on the fly
iAPBS: Grid values:
iAPBS: fglen: 13.346 17.483 9.556
iAPBS: cglen: 13.346 17.483 9.556
iAPBS: dime: 33 33 33
iAPBS: grid: 0.500 0.500 0.500
iAPBS: Required memory (in MB): 6.854
APBS calculation parameters:
Nonlinear traditional PBE
Single Debye-Hukel boundary conditions
Cubic-spline surface
Using cubic B-spline discretization
Grid dimension: 33 33 33
Coarse grid lengths: 13.346 17.483 9.556 A
Fine grid lengths: 13.346 17.483 9.556 A
Grid spacings: 0.500 0.500 0.500 A
Solute dielectric (pdie): 2.000
Solvent dielectric (sdie): 78.400
Temperature: 298.150 K
Surface sphere density (sdens): 10.000 grid points/A^2
Surface tension: 0.105 kJ/mol/A
Using charge/radii information from prmtop file
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.3630E+02 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = 244.2636
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 6.9045
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.3630E+02 5.3610E+00 1.8943E+01 N 7
BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071
VDWAALS = 2.8120 EEL = -80.1238 EPB = 244.2636
1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000
ENPOLAR = 6.9045
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.01 ( 1.47% of Total)
| Gen Born time 0.00 ( 0.01% of Nonbo)
| PB Nonbond 0.50 (100.0% of Nonbo)
| Nonbond force 0.50 (100.0% of Force)
| Bond/Angle/Dihedral 0.00 ( 0.02% of Force)
| Other 0.00 ( 0.01% of Force)
| Force time 0.50 (100.0% of Runmd)
| Runmd Time 0.50 (89.67% of Total)
| Other 0.05 ( 8.85% of Total)
| Total time 0.55 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 14:28:33.049 on 05/28/2008
| Setup done at 14:28:33.106 on 05/28/2008
| Run done at 14:28:33.602 on 05/28/2008
| wallclock() was called 22 times

13
contrib/iapbs/modules/Amber/test/apbs_min/2ala.prmcrd Normal file
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@@ -0,0 +1,13 @@
ACE
22
2.0000010 1.0000000 -0.0000013 2.0000010 2.0900000 0.0000001
1.4862640 2.4538490 0.8898240 1.4862590 2.4538520 -0.8898200
3.4274200 2.6407950 -0.0000030 4.3905800 1.8774060 -0.0000066
3.5553754 3.9696488 -0.0000031 2.7331200 4.5561601 -0.0000013
4.8532621 4.6139253 -0.0000043 5.4075960 4.3155388 0.8898151
5.6613044 4.2208425 -1.2321480 5.1232615 4.5213630 -2.1312016
6.6304840 4.7189354 -1.2057908 5.8085401 3.1408723 -1.2413850
4.7126759 6.1294185 0.0000014 3.6006445 6.6527027 0.0000062
5.8460533 6.8348833 0.0000025 6.7370014 6.3591620 -0.0000004
5.8460551 8.2838837 0.0000062 4.8185761 8.6477349 0.0000104
6.3597984 8.6477313 0.8898282 6.3597900 8.6477354 -0.8898188

229
contrib/iapbs/modules/Amber/test/apbs_min/2ala.prmtop Normal file
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@@ -0,0 +1,229 @@
%VERSION VERSION_STAMP = V0001.000 DATE = 10/18/06 21:21:36
%FLAG TITLE
%FORMAT(20a4)
ACE
%FLAG POINTERS
%FORMAT(10I8)
22 7 12 9 25 11 42 18 0 0
99 3 9 11 18 8 16 16 7 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
HH32HH33
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
1.77849648E+00 1.77849648E+00
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 1 3 4 5 6 2 7
2 1 1 1 3 4 5 6 2 7
7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
6 7 4 3 7 3 10 4 10 7
6 3 2 1 7 3 5 4 3 2
1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 2 3 5
8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
21 27 22 23 24 25 26 27 28
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ACE ALA NME
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 7 17
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
3.10000000E+02 4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
1.52600000E+00 1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01
8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01
5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01
3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00
1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 5.30000000E-01 1.50000000E-01
5.00000000E-01 8.00000000E-01 8.50000000E-01 8.00000000E-02 1.55555556E-01
7.00000000E-02 1.00000000E-01 1.70000000E+00 2.00000000E+00 1.05000000E+01
1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00
2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
6.20665997E+04 5.94667300E+01 3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.13252061E+02 1.93248820E+00 1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
3 6 3 3 9 3 0 3 3 30
33 3 30 36 3 30 39 3 24 27
5 18 21 7 54 57 5 54 60 5
54 63 5 48 51 7
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 15 1 12 18 2 3 12 4 42
45 1 42 48 2 24 30 6 24 42
4 18 24 8 48 54 8
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
12 18 21 2 9 3 12 4 6 3
9 5 6 3 12 4 0 3 6 5
0 3 9 5 0 3 12 4 42 48
51 2 36 30 39 5 33 30 36 5
33 30 39 5 27 24 30 9 27 24
42 10 24 30 33 11 24 30 36 11
24 30 39 11 21 18 24 12 18 24
27 13 60 54 63 16 57 54 60 16
57 54 63 16 51 48 54 12 48 54
57 13 48 54 60 13 48 54 63 13
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 1 12 18 24 3 3 12
15 6 3 12 18 7 45 42 48 1
42 48 54 3 30 24 42 8 24 42
45 6 24 42 48 7 18 24 30 14
18 24 42 15
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
15 12 18 21 1 15 12 -18 21 2
12 18 24 27 3 9 3 12 15 7
9 3 -12 15 3 9 3 -12 15 9
9 3 12 18 3 6 3 12 15 7
6 3 -12 15 3 6 3 -12 15 9
6 3 12 18 3 3 12 18 21 2
0 3 12 15 7 0 3 -12 15 3
0 3 -12 15 9 0 3 12 18 3
45 42 48 51 1 45 42 -48 51 2
42 48 54 57 3 42 48 54 60 3
42 48 54 63 3 39 30 24 42 10
36 30 24 42 10 33 30 24 42 10
27 24 30 33 10 27 24 30 36 10
27 24 30 39 10 27 24 42 45 7
27 24 -42 45 9 27 24 42 48 3
24 42 48 51 2 21 18 24 27 3
21 18 24 30 3 21 18 24 42 3
18 24 30 33 10 18 24 30 36 10
18 24 30 39 10 51 48 54 57 3
51 48 54 60 3 51 48 54 63 3
12 24 -18 -21 16 42 54 -48 -51 16
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 24 2 12 18 24 30 4
12 18 -24 30 3 12 18 -24 30 5
12 18 -24 30 6 12 18 24 42 7
12 18 -24 42 8 3 12 18 24 2
45 42 48 54 2 30 24 42 45 3
30 24 42 48 11 30 24 -42 48 12
24 42 48 54 2 18 24 42 45 3
18 24 42 48 13 18 24 -42 48 14
3 18 -12 -15 15 24 48 -42 -45 15
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 3 4 5 6
7 8 9 4 5 6 7 5 6 7
6 7 8 9 10 11 15 7 8 9
8 9 10 11 12 13 14 15 16 17
9 10 11 15 10 11 12 13 14 15
16 17 18 19 11 12 13 14 15 16
17 12 13 14 15 16 17 13 14 15
14 15 15 16 17 18 19 20 21 22
17 18 19 18 19 20 21 22 19 20
21 22 20 21 22 21 22 22 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1
H1 H1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E M E M E M E 3 E E E M E M E M E
E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01

12
contrib/iapbs/modules/Amber/test/apbs_min/Run.apbs.min Normal file
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@@ -0,0 +1,12 @@
#!/bin/sh
export MCSH_HOME=/dev/null
output=minim.out
$TESTsander -O -i minim.in -c 2ala.prmcrd -p 2ala.prmtop -o $output
$AMBERHOME/test/dacdif $output.save $output
/bin/rm -f mdinfo restrt

20
contrib/iapbs/modules/Amber/test/apbs_min/minim.in Normal file
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@@ -0,0 +1,20 @@
APBS minim test
&cntrl
maxcyc=100, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_debug = 0, apbs_print=0,
dime = 33, 33, 33,
cglen = 17.0071, 13.8706, 12.3012,
fglen = 17.0071, 13.8706, 12.3012,
cmeth=1,
bcfl=1,
srfm=2,
chgm=1,
pdie=2.0,
sdie=78.54,
radiopt=2, pqr='pqr',
&end

1080
contrib/iapbs/modules/Amber/test/apbs_min/minim.out.save Normal file
View File

File diff suppressed because it is too large Load Diff

1079
contrib/iapbs/modules/Amber/test/apbs_min/minim.out.save.amber9 Normal file
View File

File diff suppressed because it is too large Load Diff

22
contrib/iapbs/modules/Amber/test/apbs_min/pqr Normal file
View File

@@ -0,0 +1,22 @@
ATOM 1 HH31 ACE 1 2.000 1.000 -0.000 0.1123 1.4870
ATOM 2 CH3 ACE 1 2.000 2.090 0.000 -0.3662 1.9080
ATOM 3 HH32 ACE 1 1.486 2.454 0.890 0.1123 1.4870
ATOM 4 HH33 ACE 1 1.486 2.454 -0.890 0.1123 1.4870
ATOM 5 C ACE 1 3.427 2.641 -0.000 0.5972 1.9080
ATOM 6 O ACE 1 4.391 1.877 -0.000 -0.5679 1.6612
ATOM 7 N ALA 2 3.555 3.970 -0.000 -0.4157 1.8240
ATOM 8 H ALA 2 2.733 4.556 -0.000 0.2719 0.6000
ATOM 9 CA ALA 2 4.853 4.614 -0.000 0.0337 1.9080
ATOM 10 HA ALA 2 5.408 4.316 0.890 0.0823 1.3870
ATOM 11 CB ALA 2 5.661 4.221 -1.232 -0.1825 1.9080
ATOM 12 HB1 ALA 2 5.123 4.521 -2.131 0.0603 1.4870
ATOM 13 HB2 ALA 2 6.630 4.719 -1.206 0.0603 1.4870
ATOM 14 HB3 ALA 2 5.809 3.141 -1.241 0.0603 1.4870
ATOM 15 C ALA 2 4.713 6.129 0.000 0.5973 1.9080
ATOM 16 O ALA 2 3.601 6.653 0.000 -0.5679 1.6612
ATOM 17 N NME 3 5.846 6.835 0.000 -0.4157 1.8240
ATOM 18 H NME 3 6.737 6.359 -0.000 0.2719 0.6000
ATOM 19 CH3 NME 3 5.846 8.284 0.000 -0.1490 1.9080
ATOM 20 HH31 NME 3 4.819 8.648 0.000 0.0976 1.3870
ATOM 21 HH32 NME 3 6.360 8.648 0.890 0.0976 1.3870
ATOM 22 HH33 NME 3 6.360 8.648 -0.890 0.0976 1.3870

61
contrib/iapbs/modules/Amber/test/apbs_radi/Run.ion.min Normal file
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@@ -0,0 +1,61 @@
#!/bin/csh -f
if( ! $?TESTsander ) set TESTsander = "../../exe/sander.APBS"
if( ! $?DO_PARALLEL ) then
setenv DO_PARALLEL " "
else
echo "This test not set up for parallel"
echo " cannot run in parallel with pbsa"
exit 0
endif
setenv MCSH_HOME /dev/null
if ( -e mdin ) then
rm mdin
endif
cat > mdin <<EOF
test of iAPBS/sander solvation energies (based on pbsa_radi)
&cntrl
ntx=1, irest=0,
imin=1, maxcyc=0,
ntpr=1, ntwr=100000,
igb=6, ntb=0,
ntc=1, ntf=1, tol=0.000001,
ntt=0, temp0=300
&end
&apbs
apbs_debug=0,
apbs_print=0,
grid=0.5, 0.5, 0.5,
calc_type=0,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=80.0,
srad = 1.4,
radiopt=0,
calcforce=0, calcnpenergy=1,
&end
EOF
set all = "Li Na K Rb Cs F Cl IM Br I MG Ca Zn tp3 ile leu val phe trp hid hie nhe tyr ser thr cys cyx met lyn ash glh asn gln nma alabk glybk probk da dc dg dt ru arg asp cym glu hip lys dap da3p da5p danp rap ra3p ra5p ranp"
foreach aa ($all)
set output = $aa.out
$DO_PARALLEL $TESTsander -O -i mdin -p ./prmtop-inpcrd/$aa.prmtop -c ./prmtop-inpcrd/$aa.inpcrd -o $output < /dev/null || goto error
${AMBERHOME}/test/dacdif ./out.save/$aa.out.save $output
/bin/rm -f restrt mdinfo mdcrd
goto next
error:
echo " ${0}: Program error"
exit(1)
next:
end

189
contrib/iapbs/modules/Amber/test/apbs_radi/out.save/Br.out.save Normal file
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@@ -0,0 +1,189 @@
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 05/28/2008 at 14:02:30
[-O]verwriting output
File Assignments:
| MDIN: mdin
| MDOUT: Br.out
|INPCRD: ./prmtop-inpcrd/Br.inpcrd
| PARM: ./prmtop-inpcrd/Br.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
test of iAPBS/sander solvation energies (based on pbsa_radi)
&cntrl
ntx=1, irest=0,
imin=1, maxcyc=0,
ntpr=1, ntwr=100000,
igb=6, ntb=0,
ntc=1, ntf=1, tol=0.000001,
ntt=0, temp0=300
&end
&apbs
apbs_debug=0,
apbs_print=0,
grid=0.5, 0.5, 0.5,
calc_type=0,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=80.0,
srad = 1.4,
radiopt=0,
calcforce=0, calcnpenergy=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 12/05/05 Time = 17:24:50
NATOM = 1 NTYPES = 1 NBONH = 0 MBONA = 0
NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
NHPARM = 0 NPARM = 0 NNB = 1 NRES = 1
NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0
NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0
IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 194
| Hollerith 9
| Integer 20018
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 79 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
Cl-
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 100000
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 6, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
Cl-
begin time read from input coords = 0.000 ps
iAPBS: Initializing APBS interface
iAPBS: Using charge/radii definition from prmtop file
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting dime re-calculation on the fly
APBS calculation parameters:
Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Smoothed molecular surface definition
Using cubic B-spline discretization
Grid dimension: 33 33 33
Coarse grid lengths: 5.100 5.100 5.100 A
Fine grid lengths: 5.100 5.100 5.100 A
Grid spacings: 0.500 0.500 0.500 A
Solute dielectric (pdie): 1.000
Solvent dielectric (sdie): 80.000
Temperature: 298.150 K
Surface sphere density (sdens): 10.000 grid points/A^2
Surface tension: 0.105 kJ/mol/A
Using charge/radii information from prmtop file
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.1591E+02 0.0000E+00 0.0000E+00 Br 1
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 0.0000 EPB = -118.5587
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
ENPOLAR = 2.6522
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.1591E+02 0.0000E+00 0.0000E+00 Br 1
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 0.0000 EPB = -118.5587
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
ENPOLAR = 2.6522
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.06% of Total)
| PB Nonbond 0.65 (100.0% of Nonbo)
| Nonbond force 0.65 (100.0% of Force)
| Force time 0.65 (100.0% of Runmd)
| Runmd Time 0.65 (99.62% of Total)
| Other 0.00 ( 0.32% of Total)
| Total time 0.65 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 14:02:30.852 on 05/28/2008
| Setup done at 14:02:30.854 on 05/28/2008
| Run done at 14:02:31.506 on 05/28/2008
| wallclock() was called 22 times

189
contrib/iapbs/modules/Amber/test/apbs_radi/out.save/Ca.out.save Normal file
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@@ -0,0 +1,189 @@
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 05/28/2008 at 14:02:32
[-O]verwriting output
File Assignments:
| MDIN: mdin
| MDOUT: Ca.out
|INPCRD: ./prmtop-inpcrd/Ca.inpcrd
| PARM: ./prmtop-inpcrd/Ca.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
test of iAPBS/sander solvation energies (based on pbsa_radi)
&cntrl
ntx=1, irest=0,
imin=1, maxcyc=0,
ntpr=1, ntwr=100000,
igb=6, ntb=0,
ntc=1, ntf=1, tol=0.000001,
ntt=0, temp0=300
&end
&apbs
apbs_debug=0,
apbs_print=0,
grid=0.5, 0.5, 0.5,
calc_type=0,
cmeth=1,
bcfl=2,
srfm=1,
chgm=1,
pdie=1.0,
sdie=80.0,
srad = 1.4,
radiopt=0,
calcforce=0, calcnpenergy=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 12/05/05 Time = 17:20:25
NATOM = 1 NTYPES = 1 NBONH = 0 MBONA = 0
NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
NHPARM = 0 NPARM = 0 NNB = 1 NRES = 1
NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0
NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0
IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 194
| Hollerith 9
| Integer 20018
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 79 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
MG2
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 100000
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 6, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
MG2
begin time read from input coords = 0.000 ps
iAPBS: Initializing APBS interface
iAPBS: Using charge/radii definition from prmtop file
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting dime re-calculation on the fly
APBS calculation parameters:
Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Smoothed molecular surface definition
Using cubic B-spline discretization
Grid dimension: 33 33 33
Coarse grid lengths: 5.780 5.780 5.780 A
Fine grid lengths: 5.780 5.780 5.780 A
Grid spacings: 0.500 0.500 0.500 A
Solute dielectric (pdie): 1.000
Solvent dielectric (sdie): 80.000
Temperature: 298.150 K
Surface sphere density (sdens): 10.000 grid points/A^2
Surface tension: 0.105 kJ/mol/A
Using charge/radii information from prmtop file
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.8667E+02 0.0000E+00 0.0000E+00 Ca 1
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 0.0000 EPB = -389.7040
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
ENPOLAR = 3.0306
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.8667E+02 0.0000E+00 0.0000E+00 Ca 1
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 0.0000 EPB = -389.7040
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
ENPOLAR = 3.0306
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.06% of Total)
| PB Nonbond 0.65 (100.0% of Nonbo)
| Nonbond force 0.65 (100.0% of Force)
| Force time 0.65 (100.0% of Runmd)
| Runmd Time 0.65 (99.64% of Total)
| Other 0.00 ( 0.29% of Total)
| Total time 0.66 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 14:02:32.911 on 05/28/2008
| Setup done at 14:02:32.913 on 05/28/2008
| Run done at 14:02:33.569 on 05/28/2008
| wallclock() was called 22 times

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