Author: Holger Gohlke
Date: 01/30/03

Programs: mm_pbsa.pl

Description: pdb file was parsed as space-separated column file, not as
             fixed column file.  

Severity: mm_pbsa.pl fails if non-space-separated columns exist

Fix:  apply the following patch to amber7/src/mm_pbsa/mm_pbsa.pl

*** mm_pbsa.pl	Thu Jan 30 08:41:20 2003
--- mm_pbsa.pl	Thu Jan 30 15:09:30 2003
***************
*** 1311,1334 ****
      chomp($line);
      my $rad;
      if($line =~ /(ATOM|HETATM)/){
!       #          ATOM              1      N        MET    1        19.192      38.199      15.560
!       #          $1                $2     $3   $4  $5   $6     $7  
!       $line =~ /(ATOM +|HETATM +)(\d+ +)(\S+)( +)(\S+)( +\d+)( +-?\d+\.\d+ +-?\d+\.\d+ +-?\d+\.\d+)/;
!       my $card = $1;
!       my $atnum = $2;
!       my $atm = $3;
!       my $spc = $4;
!       my $res = $5;
!       my $resnum = $6;
!       my $crd = $7;
!  
!       # Special treatment of H's not necessary -> done by atm-pattern
        # Caveat: He, Hf, Hg not recognized as such
!       
        my $found = 0;
        my $r_arr;
        foreach $r_arr (@$r_pat){
!         if($res =~ /$r_arr->[0]/ && $atm =~ /$r_arr->[1]/){
            $rad = $exp_h ? $r_exp_rad->{$r_arr->[2]} : $r_unit_rad->{$r_arr->[2]};
            $found = 1;
            last;
--- 1311,1331 ----
      chomp($line);
      my $rad;
      if($line =~ /(ATOM|HETATM)/){
!       my(        $card, $atnum, $atm1, $atm2, $alt, $resname, $resno, $x, $y, $z) = 
!          unpack("a6     a5 x    a      a3     a     a3 x2     a4 x4   a8  a8  a8", $line);
! 
!       # Special treatment of H's not necessary -> done by atm-pattern    
        # Caveat: He, Hf, Hg not recognized as such
!       my $atm = $atm1 . $atm2;
!       my $restmp = $resname;
!       $restmp =~ s/\s//g; # Remove leading and trailing white spaces because patterns below
!       my $atmtmp = $atm;  #   are of the type /^\S+$/
!       $atmtmp =~ s/\s//g;
! 
        my $found = 0;
        my $r_arr;
        foreach $r_arr (@$r_pat){
!         if($restmp =~ /$r_arr->[0]/ && $atmtmp =~ /$r_arr->[1]/){
            $rad = $exp_h ? $r_exp_rad->{$r_arr->[2]} : $r_unit_rad->{$r_arr->[2]};
            $found = 1;
            last;
***************
*** 1336,1350 ****
        }
  
        if(! $found){
!         print "        No radius found for $atnum $res $atm\n";
          die();
        }
  
!       print PQR $card,$atnum,$res,$spc,$atm,$resnum,$crd,"  00.000  ",$rad,"\n";
!     }
!     else{
!       print PQR $line,"\n";
      }
    }
    close(PQR);
    close(PDB);
--- 1333,1351 ----
        }
  
        if(! $found){
!         print "        No radius found for $atnum $resname $atm\n";
          die();
        }
  
!       $line = sprintf("%-6s%5d %1s%-3s%1s%-3s  %4d    %8.3f%8.3f%8.3f%6.2f%6.2f",
!                        $card, 
!                            $atnum, 
!                                $atm1, $atm2, 
!                                       $alt, 
!                                          $resname, 
!                                                $resno,$x,  $y,  $z,  "00.000", $rad);
      }
+     print PQR $line,"\n";
    }
    close(PQR);
    close(PDB);

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Temporary workarounds: none