Automatic Solvate and Parameterization Script for GROMACS

#!/usr/bin/perl
#
#
# Simple script to solvate and parameterize a protein
# Using GROMACS
# genion line needs to change to match your neutralization conditions
# you also need your own mdp file
# ./gromacser.pl <name of pdb>


($a, $b) = split(/\./,$ARGV[0]);

`pdb2gmx -f $ARGV[0] -ff oplsaa -o init.$ARGV[0] -p $a.top`;

`editconf -bt cubic -f init.$ARGV[0] -o box.gro -c -d 0.7`;

`genbox -cp box.gro -cs spc216.gro -o b4ion.gro -p $a.top`;

`grompp -f em.mdp -c b4ion.gro -p $a.top -o b4ion.tpr`;

`genion -s b4ion.tpr -o b4em.gro -nname Cl -nn 1 -p $a.top`;


`grompp -f em.mdp -c b4em.gro -p $a.top -o em.tpr`;