#!/usr/bin/perl

# fix-gromacs < foo.gromacs.pdb > foo.gromacs-fixed.pdb
# fixes some of the atom naming that gromacs gets wrong

while(<STDIN>)
{
    s/ CD  ILE/ CD1 ILE/;
    s/ O1  / O   /;
    s/ O2  / OXT /;
    print;
}

exit(0);