Computational Drug Discovery and Design

then

LIGFILE="lig.prmtop"

fi

echo -n "Trajectory file (name with ext.): "

read MDCRD

if [ -z "$MDCRD" ]

then

echo "*** Error: Trajectory files must be specified expli-

citly."

exit

fi

echo -n "Number of CPUs to use: [4] "

read NPROC

if [ -z $NPROC ]

then

NPROC=4

fi

echo "Launching MMPBSA.py.MPI on $NPROC CPUs."

echo -n "JOB STARTED on "

date

mpiexec -np $NPROC $AMBERHOME/bin/MMPBSA.py.MPI -O -i $IN-

SCRIPT \

-o out_binding.dat \

-do out_decomp.dat \

-sp $SYSFILE \

-cp $CPLFILE \

-rp $RECFILE \

-lp $LIGFILE \

-y $MDCRD>out.log

echo -n "JOB FINISHED on "

date

exit 0

Note that there are two output files with predefined names:
out_binding.dat and out_decomp.dat. The first one contains infor-
mation on binding energies and the second one lists energy decom-
position details. An example of the input script for per-residue
energy decomposition (mmpbsa_py.in) is given below:

MMPBSA input file for running per-residue decomposition
&general
startframe=3001, endframe=5000, interval=2,

Molecular Dynamics in Virtual Screening 171