Computational Drug Discovery and Design

the protein and of the ligand. In practice, this information is

extracted from the MD trajectory of the solvated protein–ligand

complex. Consequently, the program requires the corresponding

topologies, which have already been generated with tleap in inter-

mediate steps of the procedure (files named sys.prmtop, cpl.

prmtop, rec.prmtop, and lig.prmtop, corresponding to the solvated

system, the unsolvated complex, the receptor, and the ligand,

respectively).

1. Use the MMPBSA.py.MPI [62] program to profit from multi-
   core systems. The script below demonstrates its use in calculat-
   ing the protein–ligand intermolecular energy with both the
   MM-PBSA and the MM-GBSA methods:

#!/bin/sh

echo -n "Input script name: [mmpbsa_py.in] "

read INSCRIPT

if [ -z $INSCRIPT ]

then

INSCRIPT="mmpbsa_py.in"

fi

echo -n "Solvated prmtop file: [sys.prmtop] "

read SYSFILE

if [ -z $SYSFILE ]

then

SYSFILE="sys.prmtop"

fi

echo -n "Complex prmtop file: [cpl.prmtop] "

read CPLFILE

if [ -z $CPLFILE ]

then

CPLFILE="cpl.prmtop"

fi

echo -n "Receptor prmtop file: [rec.prmtop] "

read RECFILE

if [ -z $RECFILE ]

then

RECFILE="rec.prmtop"

fi

echo -n "Ligand prmtop file: [lig.prmtop] "

read LIGFILE

if [ -z $LIGFILE ]

170 Gre ́gory Menchon et al.