AMBER Archive (2004)

Subject: AMBER: mm_PBSA: problems calculating molecular surface for some snapshots

From: Magne Olufsen (Magne.Olufsen_at_chem.uit.no)
Date: Mon Nov 08 2004 - 03:50:39 CST

I am trying to calculate the stability of a protein with the mm_pbsa script
(AMBER 7), the script wont calculate the molecular surface for some
snapshots. I got this message in the mm_pbsa.out:
  Reading cod_com.all.out
     Entry 0 PB PB 0 exists -> overwriting
     Entry 0 PB PB 1 exists -> overwriting
     Entry 0 PB PB 2 exists -> overwriting
     Entry 0 PB PB 3 exists -> overwriting
     Entry 0 PB PB 4 exists -> overwriting
     Entry 0 PB PB 5 exists -> overwriting
     Entry 0 PB PB 6 exists -> overwriting
     Entry 0 PB PB 7 exists -> overwriting
     Entry 0 PB PB 8 exists -> overwriting
     Entry 0 PB PB 9 exists -> overwriting
     Entry 0 PB PB 10 exists -> overwriting
     Entry 0 PB PB 11 exists -> overwriting
     Entry 0 PB PB 12 exists -> overwriting
     Entry 0 PB PB 13 exists -> overwriting
     Entry 0 PB PB 14 exists -> overwriting
     Entry 0 PB PB 52 exists -> overwriting
     Entry 0 PB PB 53 exists -> overwriting
     Entry 0 PB PB 54 exists -> overwriting
     Entry 0 PB PB 55 exists -> overwriting
     Entry 0 PB PB 56 exists -> overwriting
     Entry 0 PB PB 57 exists -> overwriting
     Entry 0 PB PB 58 exists -> overwriting
     Entry 0 PB PB 59 exists -> overwriting
     Entry 0 PB PB 60 exists -> overwriting
     Entry 0 PB PB 61 exists -> overwriting
     Entry 0 PB PB 62 exists -> overwriting
     WARNING: Missing SURF for MS in 62 -> Taken from 61
     Entry 0 PB PB 63 exists -> overwriting

I have read that others have had this problem
http://structbio.vanderbilt.edu/archives/amber-archive/2004/0668.phtml and
it was recomanded to:
"comment the line "unlink $mol;" in the subroutine calc_ms in mm_pbsa.pl.
Similarly, you may want to comment the other "unlink ..." lines in the
calc_... routines in mm_pbsa.pl."

I have tried to do comment two lines in the mm_pbsa.pl file, but still I
got the same error message:
Under you can see which lines I have comment:

sub calc_ms($out,$pqr,$mol,$r_mol,$r_pro){
##########################################

   my $OUT = shift;
   my $pqr = shift;
   my $mol = shift;
   my $r_mol = shift;
   my $r_pro = shift;

   print " Calc MS\n";
   my $command = $r_pro->{"MS"} . " $pqr " . $r_mol->{"PROBE"} . " > " . $mol;
   system($command);

   open(IN,"$mol") || die(" $mol not opened\n");
   my $line;
   while(defined($line = <IN>)){
     if($line =~ /surface area =/){
       print OUT $line;
     }
   }
   close(IN);

   #unlink $pqr;
   #unlink $mol;

Does anyone know what could be wrong???

Greetings from Magne Olufsen
Univ. of Tromsų, Norway

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