correct_3pt_pdb.pl

#! /usr/bin/perl -w
# This perl script creates input file for PAS (Palo Alto Sampler)
# In A.pdb generated by extract_3pt_pdb.pl GLY's GCA and GCMA has 
# the same coordinates. This script modifies GCMA coordinate by
# eps = 1.e-3, so that GCA and GCMA does not coincide. This will
# remove any incompatibility with PAS topology
# Usage:
# ./correct_3pt_pdb.pl A.pdb > Ac.pdb

use Math::Trig;

$pdb = $ARGV[0];
open(PDB,"$pdb");

$eps = 0.01;

while (<PDB>) {
      chomp;
      $entry = $_;
      if (substr($entry,0,4) eq 'ATOM') {
         $altLoc = substr($entry,16,1);
         if ($altLoc eq ' ' || $altLoc eq 'A') {
            @list_entry = split;   
            $atom = $list_entry[2];
            $resName = substr($entry,17,3); 
            $chainID = substr($entry,21,1); $chainID =~ tr/ //d;
            $resSeq  = substr($entry,22,4); $resSeq =~ tr/ //d;
            $x = substr($entry,30,8); $x =~ tr/ //d;
            $y = substr($entry,38,8); $y =~ tr/ //d;
            $z = substr($entry,46,8); $z =~ tr/ //d;
            if ($resName eq 'GLY' && $atom eq 'CMA') {
               $x += $eps; 
               $x_field = sprintf("%8s",$x);
               substr($entry,30,8) = $x_field;   
            }
            print "$entry\n";
	 }
      } 
      else {
         print "$entry\n";
      }
      if (substr($entry,0,3) eq 'END' || substr($entry,0,3) eq 'TER') {
         last;
      }
}