iAPBS/Amber Interface: User Guide

To compile iAPBS/Amber interface two packages are required:

• APBS (version 3.4.1 or later).
• AmberTools (version 23 or later)

Building of the iAPBS interface requires compilation and installation of MALOC and APBS libraries. The following describes all steps (assumes bash as login script, modify appropriately for t/csh). The instructions also assume working gcc/gfortran compilers. The use of Intel compilers is recomended for better performance of the compiled executables.

# create a build directory and cd to it, then:
export APBS_PREFIX=`pwd`
export APBSHOME=$APBS_PREFIX/apbs
export APBS_SRC=$APBS_PREFIX/apbs-pdb2pqr/apbs
export MCSH_HOME=/dev/null

# get the source
git clone https://github.com/Electrostatics/apbs-pdb2pqr
cd apbs-pdb2pqr
git submodule init
git submodule update

# configure and build it
cd $APBS_PREFIX
mkdir build.apbs && cd $_
cmake -DCMAKE_INSTALL_PREFIX=$APBSHOME \
 -DCMAKE_BUILD_TYPE=Release \
 -DBUILD_DOC=OFF \
 -DBUILD_SHARED_LIBS=OFF \
 -DENABLE_QUIET=ON \
 -DENABLE_iAPBS=ON \
 $APBS_SRC

make install

These steps should build the apbs executable in ${APBSHOME}/bin and all the necessary apbs and iapbs libraries in ${APBSHOME}/lib.

The Amber/APBS module is supported on the x86_64 Linux platform only.

# unpack your Amber and Amber Tools source code in
# ${APBS_PREFIX}/amber (or use a symlink), then:

export AMBERHOME=$APBS_PREFIX/amber.apbs
export AMBER_SRC=$APBS_PREFIX/amber

cd $APBS_PREFIX
mkdir build.amber && cd $_
cmake3 -DCMAKE_INSTALL_PREFIX=$AMBERHOME \
       -DCOMPILER=GNU \
       -DMPI=FALSE \
       -DCUDA=FALSE \
       -DBUILD_PYTHON=FALSE \
       -DDOWNLOAD_MINICONDA=FALSE \
       -DBUILD_GUI=FALSE \
       -DCHECK_UPDATES=FALSE \
       -DINSTALL_TESTS=TRUE \
       -DBUILD_SANDER_APBS=TRUE \
       -DPRINT_PACKAGING_REPORT=TRUE \
       -DCMAKE_PREFIX_PATH=$APBSHOME \
       $AMBER_SRC

make -j 16 # or how many CPU cores you have available
make install

# And test it:

export TESTsander=${AMBERHOME}/bin/sander.APBS
cd ${AMBERHOME}/test/iapbs_radi
./Run.ion.min

This builds the sander.APBS binary in $AMBERHOME/bin directory.

Instructions for Amber 18 or earlier:

# unpack your Amber and Amber Tools source code in
# ${APBS_PREFIX}/amber (or use a symlink), then:

cd $APBS_PREFIX
export AMBERHOME=${APBS_PREFIX}/amber
cd $AMBERHOME
./configure -noX11 --skip-python gnu
make install

cd ${AMBERHOME}/AmberTools/src/sander
export APBS_LIBDIR=${APBS_PREFIX}/lib
export APBS_LIBS="-liapbs -lapbs_routines -lapbs_mg -lapbs_generic -lapbs_pmgc -lmaloc -lz"
make clean
make depend
make -e AMBERBUILDFLAGS="-DAPBS" ${AMBERHOME}/bin/sander.APBS

# test it
export TESTsander=${AMBERHOME}/bin/sander.APBS
cd ${AMBERHOME}/test/iapbs_radi
./Run.ion.min

Note

• Values in square brackets [] are defaults. For up-to-date default values please see $AMBERHOME/src/sander/apbs.F90
• To disable creation of io.mc file before attempting any extensive minimization or MD simulation with the APBS module please set the MCSH_HOME environment variable to /dev/null (export MCSH_HOME=/dev/null).

This example executes a solvation energy calculation and prints out total solvation energy for the given molecule (in energy terms EPB and ENPOLAR for polar and non-polar solvation terms, respectively).

iAPBS solvation energy example
&cntrl
  maxcyc=0, imin=1,
  cut=12.0,
  igb=6, ntb=0,
  ntpr=1,
/
&apbs
   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,
   nion=2,
   ionq= 1.0, -1.0,
   ionc= 0.15, 0.15,
   ionrr= 2.0, 2.0,
   radiopt=3, pqr='my.pqr',
   calcforce=0, calcnpenergy=1,
&end

This example executes a single point electrostatic energy calculation and prints out the calculated energy (in energy terms EPB and ENPOLAR for polar and non-polar terms, respectively).

APBS electrostatic energy example
&cntrl
  maxcyc=0, imin=1,
  cut=12.0,
  igb=6, ntb=0,
  ntpr=1,
/
&apbs
   apbs_print=1
   grid= 0.1, 0.5, 0.5,
   calc_type=0, cmeth=1,
   sp_apbs=.true.,
&end

This examples shows how to use the Amber/APBS module for carrying out a molecular dynamics simulation in implicit solvent with APBS.

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,
    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='my.pqr',
    calcforce=2, calcnpenergy=1,
    nion=2,
    ionq= 1.0, -1.0,
    ionc= 0.15, 0.15,
    ionrr= 2.0, 2.0,
 &end

When this input file is run three DX files will be created. These can be visualized using several applications (for details please see APBS visualization guide). The DX files will be iapbs-pot.dx, iapbs-smol.dx and iapbs-charge.dx which will contain electrostatic potential, solvent accessible surface and charge information, respectively.

APBS visualization example
&cntrl
  maxcyc=0, imin=1,
  cut=12.0,
  igb=6, ntb=0
  ntpr=1,
/
&apbs
   apbs_print=1,
   grid= 0.5, 0.5, 0.5,
   calc_type=0,
   srad=0.7,
   wpot=1, wchg=1, wsmol=1,
   sp_apbs=.true.,
&end

Note

To determine the correct size of the numerical grid enveloping the studied molecule (parameters cglen and fglen) you can use psize.py tool from the APBS distribution.

Parameter sp_apbs=.true. triggers only a single APBS calculation (SP, single point energy). The calculated electrostatic energy contains self-energy terms thus it is not very useful by itself. This is however useful when, for instance, generating DX files for visualization. If the parameter sp_apbs is omitted (or set to .false., which is the default) then two APBS calculations (one for a system in solvent and then in vacuum) are performed every time solvation energy and forces are recalculated. This is used during minimization and MD simulations.