top2psf.pl

#!/usr/bin/perl

# Adapted from Graham Smith's script gmx2mmc
# modified by Marc Baaden (080901)

# this script makes a Charmmm/Xplor psf file from a GROMACS .top file
# it uses atom types, charges, masses and bond information !

$psf_res_offset=0; 

%arghash=@ARGV;
$topfile=$arghash{"-p"}; 
$pdbfile=$arghash{"-P"}; 
$psffile=$arghash{"-o"}; 

$usage_message="
NAME
        Perl script c_top2psf.pl MB080901a
 
SYNOPSIS
        c_top2psf.pl -p <topfile> -o <psffile>
        c_top2psf.pl -P <pdbfile> -o <psffile>
 
        This is a perl script to convert a GROMACS topology file
        (.TOP/.ITP)  or alternatively  a  PDB  file with Connect
	records  in  a Charmmm/Xplor  psf file  using the infor-
	mation about atom types, charges, masses and bonds. Then
	one can use VMD to visualize pdb+psf and verify whether
	the bonding topology is ok.
 
OPTIONS
        -p <topfile>
                <topfile> is a  gromacs topology file as produced
	by pdb2gmx (or it could be an itp),  containing atom type
	and charge information (no #include'd files please!)
 
 	-P <pdbfile>
		<pdbfile> is a file in PDB format with connect
	records. The expected format looks like
	ATOM      1 NA1  X       1      -8.849   0.122   1.276  0.000
	[..]
	CONNECT    2 CA   3 7 95
	[..]

        -o <psffile>
                <psffile> is the output solute file in MMC format
 
SETTINGS
	psf_res_offset
		this added to residue numbers, wherever they come
	from, before writing to psf file
 
AUTHOR
        Marc Baaden <baaden\@smplinux.de>, based on a script by
        Graham Smith.
\n"; 

###
### Command line arguments and initial info
###

# check arguments 
if ( $#ARGV != 3 || ($topfile eq "" && $pdbfile eq "") || $psffile eq "" ) { 
  die "$usage_message"; 
}

if ($topfile) { print "\nconverting from gmx top.... $topfile\n";
} elsif ($pdbfile) { print "\nconverting from PDB........ $pdbfile\n";};

# print a bit of info about non-command-line arguments
print "\npsf_res_offset............. $psf_res_offset\n"; 
print "\nreading input files........ \n"; 

###
### Read input files and open output PSF
###

# in case of a PDB file, we only read relevant lines
if ($pdbfile) { $starttop=0;
open(TOP,"$pdbfile") || die "cant open $pdbfile $usage_message"; 
 } elsif ($topfile) {
open(TOP,"$topfile") || die "cant open $topfile $usage_message"; 
};
while(my $line=<TOP>) {
	# Parsing for Gromacs topology
	if ($topfile) {
	unless ($line =~ /^\s*(#|;|$)/) {
                ### Calculate some indices
		if    ($line =~ /\[\s*atoms\s*\]/) {$starttop=@toplines}
		elsif ($line =~ /\[\s*bonds\s*\]/) {$finishtop=@toplines}
		elsif ($line =~ /\[\s*pairs\s*\]/) {$finishbon=@toplines}
		else {push @toplines,$line};
	};
	# Parsing for PDB file
	} elsif ($pdbfile) {
	unless ($line =~ /^\s*(#|;|$)/) {
                ### Calculate some indices
		if    ($line =~ /^\s*ATOM/) {
		       push @toplines,$line;
		       $finishtop=@toplines;
		       }
		elsif ($line =~ /^\s*CONNECT/) {
		       ($dummy,$atnr,$attyp,@rest)=split ' ',$line;
		       $attyplist{$atnr}=$attyp;
		       foreach $tmp (@rest) {
			 # connection info is the 2 atom numbers and 1 dummy nb
			 push @toplines,"$atnr $tmp 1";
		         }
		       $finishbon=@toplines;
		       }
		else {};
	};
	}
}
close TOP;

# append to existing psf file , or create new one
if ( -e $psffile ) { 
  # get last residue number and offset from there 
  $psf_res_offset=`tail -1 $psffile | cut -c46-50`;
  open(LINE_PSF,">>$psffile") || die "cant open $psffile $usage_message"; 
  print "appending to............... $psffile
last residue found......... $psf_res_offset"; 
} else {
  # create new psf file 
  $psf_res_offset=0;  
  open(LINE_PSF,">$psffile") || die "cant open $psffile $usage_message"; 
}

$totnbat=$finishtop-$starttop;
$totnbbd=$finishbon-$finishtop;

# debug and info - print some stuff
 print "DEBUG - starttop........... $starttop
DEBUG - finishtop.......... $finishtop
DEBUG - number of atoms.... $totnbat
DEBUG - number of bonds.... $totnbbd\n";

print "input files read...........\n\nconverting................. "; 


###
### WRITE ATOM SECTION OUTPUT
###

# set page length to a big value
select((select(LINE_PSF), $= = "999999")[0]);

for ($i=$starttop ; $i<$finishtop ; $i++)
{
# get 1 line topology info
  $_=$toplines[$i]; 
  s/^ +//g;  # remove whitespace at start of line, if any

  if ($topfile) {
  ($Tatnr,$Tattype,$Tresnr,$Tresname,$Tatname,$Tcgnr,$Tq,$Tm) = 
    split(/\s+/,$_);
  } elsif ($pdbfile) {
  ($dummy,$Tatnr,$Tatname,$Tresname,$Tresnr,$Tx,$Ty,$Tz,$Tq) = 
    split(/\s+/,$_); 
#  $Tattype="X";
  $Tattype= $attyplist{$Tatnr};
  $Tm="1.0";
  };
# output
  write (LINE_PSF); 
#      13 MAIN 1    GLN  C    C      0.260000       1.00800           0
#      23 MAIN    2  GLU    C    C  0.380000000012.0110000000
#	printf LINE_PSF ("%8d MAIN%4d%4s%4s %4s %13.10f%13.10f\n",$Tatnr,$Tresnr,$Tresname,$Tatname,$Tattype,$Tq,$Tm);
}

###
### WRITE BONDS SECTION OUTPUT
###

# write heading
select((select(LINE_PSF), $~ = "LINE_PSF_2_TOP")[0]);
write(LINE_PSF);

select((select(LINE_PSF), $~ = "LINE_PSF_2")[0]);

for ($i=$finishtop ; $i<$finishbon ; $i=$i+4)
{
	# initialize
	($Batnr1a,$Batnr1b,$Batnr2a,$Batnr2b,$Batnr3a,$Batnr3b,$Batnr4a,$Batnr4b)=("","","","","","","","");
# get 1 line topology info
# remove whitespace at start of line, if any
  $_=$toplines[$i];   s/^ +//g; ($Batnr1a,$Batnr1b,$Bfunctyp) = split(/\s+/,$_); 
  if($i+1<$finishbon) { $_=$toplines[$i+1]; s/^ +//g; ($Batnr2a,$Batnr2b,$Bfunctyp) = split(/\s+/,$_)};
  if($i+2<$finishbon) { $_=$toplines[$i+2]; s/^ +//g; ($Batnr3a,$Batnr3b,$Bfunctyp) = split(/\s+/,$_)}; 
  if($i+3<$finishbon) { $_=$toplines[$i+3]; s/^ +//g; ($Batnr4a,$Batnr4b,$Bfunctyp) = split(/\s+/,$_)}; 
# output
  write (LINE_PSF); 
}

print "done
last atom read............. $Tatnr $Tattype $Tatname
from residue............... $Tresnr $Tresname\n\n"; 

###
### FORMATS USED
###

# PSF file heading
format LINE_PSF_TOP =
PSF 
       4 !NTITLE
 REMARKS TOPOLOGY CREATED BY PERL SCRIPT (MARC BAADEN)
 REMARKS contact baaden@smplinux.de


@>>>>>>> !NATOM
$totnbat
.

# PSF file atom information
format LINE_PSF = 
##@       1 MAIN@ 1    GLN  N    N      0.260000       1.00800           0
@>>>>>>> MAIN @<<<<@<<<<@<<<<@<<<<@##.########## @##.##########
$Tatnr,$Tresnr,$Tresname,$Tatname,$Tattype,$Tq,$Tm
.	

# PSF file bond data header
format LINE_PSF_2_TOP = 

@>>>>>>> !NBOND: bonds
$totnbbd
.	

# PSF file bond data
format LINE_PSF_2 = 
@>>>>>>>@>>>>>>>@>>>>>>>@>>>>>>>@>>>>>>>@>>>>>>>@>>>>>>>@>>>>>>>
$Batnr1a,$Batnr1b,$Batnr2a,$Batnr2b,$Batnr3a,$Batnr3b,$Batnr4a,$Batnr4b
.