g_mmpbsa

Contents

• Pre-compiled binary

  • Download

  • Installation

• Installation from source code

  • Download

  • With APBS-1.3.x

  • With APBS-1.4.x

  • Without APBS (To use with external APBS)

Pre-compiled executable program

Pre-compiled program does not require any external library or GROMACS and APBS package. These programs are standalone and without any dependency. Download, extract and use it.

Download

Download Python Scripts

Installation

Extract the package. Copy g_mmpbsa and energy2bfac from bin directory to /usr/local/bin or $HOME/bin.

tar -zxvf g_mmpbsa.tar.gz
cd bin
sudo cp g_mmpbsa /usr/local/bin/.
sudo cp energy2bfac /usr/local/bin/.

or

tar -zxvf g_mmpbsa.tar.gz
cd bin
cp g_mmpbsa $HOME/bin/.
cp energy2bfac $HOME/bin/.

or

add g_mmpbsa/bin to PATH environment variable by adding following line in .bashrc file:

export PATH=${PATH}:/path/to/g_mmpbsa/bin

Installation from Source-Code

Download

1. ZIP/TAR

The ZIP file or TAR for the tool can be downloaded from github.

Also, these files can be downloaded from the left side of current webpage. After downloading the file, extract ZIP/TAR file.

2. Using git

git clone --depth 1 https://github.com/RashmiKumari/g_mmpbsa

Install with APBS-1.2.x or 1.3.x

Warning: Compiler for GROMACS, APBS and g_mmpbsa should be same.

Required Library from GROMACS: libgmx or libgromacs

Required Libraries from APBS: libapbsmainroutines, libapbs, libapbsblas, libmaloc, libapbsgen and libz.

A. Installation of GROMACS 4.5.x/4.6.x

GROMACS should be compiled and installed from the source-code.

g_mmpbsa cannot use GPU and cannot be compiled with CUDA. If CUDA is in PATH variable, GROMACS-4.6.x compiled by default with CUDA for GPU acceleration. To avoid error in g_mmpbsa compilation, use -DGMX_GPU=off with cmake during installation of GROMACS-4.6.x.

Warning: Currently, double precision GROMACS is not supported.

1. Installation of GROMACS-4.5.x

tar -zxvf gromacs-4.5.7.tar.gz
cd gromacs-4.5.7
./configure --prefix=/opt/gromacs
make
sudo make install

--prefix=/opt/gromacs specifies the path where gromacs will be installed.

2. Installation of GROMACS-4.5.7 or GROMACS-4.6.x or Gromacs-5.0.x

tar -zxvf gromacs-4.6.7.tar.gz
cd gromacs-4.6.7
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs -DGMX_GPU=off
make
sudo make install

-DCMAKE_INSTALL_PREFIX=/opt/gromacs specifies the path where gromacs will be installed.

B. Installation of APBS 1.2.x or 1.3.x

APBS should be compiled and installed from the source-code.

Warning: Downloaded binaries and libraries would not work as some required libraries are missing.

tar -zxvf apbs-1.3-source.tar.gz
cd apbs-1.3-source
./configure --prefix=/opt/apbs
make
make install

--prefix=/opt/apbs specifies the path where APBS will be installed.

C. Installation of g_mmpbsa

Follow these steps:

cd g_mmpbsa
mkdir build
cd build
cmake -DGMX_PATH=/opt/gromacs \
      -DAPBS_INSTALL=/opt/apbs \    
      -DAPBS_SRC=/path/to/apbs-1.3-source \
      -DCMAKE_INSTALL_PREFIX=/opt/g_mmpbsa \
      ..
make
make install

• -DGMX_PATH : path to GROMACS installation directory.
• -DAPBS_INSTALL: path to APBS installation directory.
• -DAPBS_SRC: path to APBS source code directroy from where APBS is configured and installed.

• -DCMAKE_INSTALL_PREFIX: path to a directory where g_mmpbsa will be installed. If this option is not provided, g_mmpbsa will install either in /usr/local/bin or in $HOME/bin directory.

• Instead of GMX_PATH and -DAPBS_INSTALL, CMAKE_PREFIX_PATH can be used before running cmake as follows. However, -DAPBS_SRC is still required.
  • export CMAKE_PREFIX_PATH=/opt/gromacs
  • export CMAKE_PREFIX_PATH=/opt/gromacs:/path/to/fftw

• In case of ERROR: FFTW library file libfftw3f.so or libfftw3f.a not found...; use -DFFTW_LIB=/path/to/fftw/lib/ to give a path for the directory containing either of the two files.

• In Gromacs-5.0.x version, if, ERROR: undefined reference to 'uncompress'. Then use: -DZLIB_PATH=/path/to/zlib.a(so).

• In Gromacs-5.0.x version, by default, TNG format trajectory support is enabled. This conflicts with the APBS-1.3 library. To resolve this problem, do either of the followings:
  • Re-install Gromacs by using -DGMX_USE_TNG=off option to disable TNG trajectory support.
  • Install with APBS-1.4 version.

Install with APBS-1.4.x

Warning: Compiler for GROMACS, APBS and g_mmpbsa should be same.

Required Library from GROMACS: libgmx or libgromacs

Required Libraries from APBS: libmaloc, libapbs_geoflow, libapbs_mg, libapbs_pmgc and libapbs_generic.

A. Install GROMACS 4.5.x/4.6.x/5.0.x

Install as described above.

B. Download and Install APBS-1.4.x

Follow these steps to download and install APBS-1.4.1 version:

# Download using git from GitHub repository
git clone -b 1.4.1-binary-release --single-branch https://github.com/Electrostatics/apbs-pdb2pqr
cd apbs-pdb2pqr
cd apbs
cd build
sh cleanup.sh
# Installation
cmake -DCMAKE_INSTALL_PREFIX=/opt/apbs -DENABLE_BEM=off -DENABLE_iAPBS=on ..
make
sudo make install

C. Installation of g_mmpbsa

cd g_mmpbsa
mkdir build
cd build
cmake -DGMX_PATH=/opt/gromacs \
      -DAPBS14=on \
      -DAPBS_INSTALL=/opt/apbs \    
      -DCMAKE_INSTALL_PREFIX=/opt/g_mmpbsa \
      ..
make
sudo make install

• -DGMX_PATH : path to GROMACS installation directory.
• -DAPBS14=on: to enable installation using APBS-1.4.x libraries
• -DAPBS_INSTALL: path to APBS installation directory.

• -DCMAKE_INSTALL_PREFIX: path to a directory where g_mmpbsa will be installed. If this option is not provided, g_mmpbsa will install either in /usr/local/bin or in $HOME/bin directory.

• Instead of GMX_PATH and -DAPBS_INSTALL, CMAKE_PREFIX_PATH can be used before running cmake as follows:
  • export CMAKE_PREFIX_PATH=/opt/gromacs:/opt/apbs
  • export CMAKE_PREFIX_PATH=/opt/gromacs:/opt/apbs:/path/to/fftw

• In case of ERROR: FFTW library file libfftw3f.so or libfftw3f.a not found...; use -DFFTW_LIB=/path/to/fftw/lib/ to give a path for the directory containing either of the two files.

• In Gromacs-5.0.x version, if, ERROR: undefined reference to 'uncompress'. Then use: -DZLIB_PATH=/path/to/zlib.a(so).

Installation without APBS (to use with external APBS)

Required Library from GROMACS: libgmx or libgromacs

A. Install GROMACS 4.5.x/4.6.x/5.0.x

Install as described above.

B. Installation of g_mmpbsa

cd g_mmpbsa
mkdir build
cd build
export CMAKE_PREFIX_PATH=/opt/gromacs
cmake -DEXT_APBS=on \
      -DCMAKE_INSTALL_PREFIX=/opt/g_mmpbsa \
      ..
make
sudo make install

• -DGMX_PATH : path to GROMACS installation directory.
• -DEXT_APBS=on: to enable installation without APBS libraries

• -DCMAKE_INSTALL_PREFIX: path to a directory where g_mmpbsa will be installed. If this option is not provided, g_mmpbsa will install either in /usr/local/bin or in $HOME/bin directory.

• In case of ERROR: FFTW library file libfftw3f.so or libfftw3f.a not found...; use -DFFTW_LIB=/path/to/fftw/lib/ to give a path for the directory containing either of the two files.

• In Gromacs-5.0.x version, if, ERROR: undefined reference to 'uncompress'. Then use: -DZLIB_PATH=/path/to/zlib.a(so).