Thanks for your answers, I also didn't really expect the hash to be the problem.
Strangely I had no error output, it just stopped. It runs rather long (~7 days), the break came after 46 hours.

Does the "time" command suppress output?
time perl createBinarySet.pl >LOG 2> ERROR &
Nothing in ERROR

The administrator didn't see anything unusal in the system logs, there was no update/restart etc.

Now I alread wrote so much, maybe you see something in the code. The script is opening a file, for example:
'/home/s0571283/positiveSet/pdb0704071050/pdb/km/pdb1kmc.ent'
hen several new files are created , in this case:

1kmc_A.pdb
1kmc_B.pdb
1kmc_C.pdb
1kmc_D.pdb
1kmc_AB.pdb
1kmc_AC.pdb
1kmc_AD.pdb
...
just contain the line starting with ATOM from original file and the matching chain ( substr($line,21,1) )

#'...or die' removed for better reading
#!/usr/bin/perl

use warnings;
use strict;
use Data::Dumper;

my(%hash);
my $startDir = '/home/s0571283/positiveSet/pdb0704071050/pdb/';

&test();
sub test(){
open(POSITIVE_CHAIN_ID, "<POSITIVE_CHAIN_ID");
#Example line:
#1KMC A B C D
   while (my $line = <POSITIVE_CHAIN_ID>){
      my @chainIDs = split(/ /,$line);
      my $pdbID = shift(@chainIDs); #1KMC
      $pdbID =~ tr/[A-Z]/[a-z]/;#1KMC -> 1kmc
      $hash{$pdbID} = [ @chainIDs ]; #1kmc-> A B C D
   }

close(POSITIVE_CHAIN_ID);
}

foreach my $key (keys %hash){print "$key\n";

   my $dir = substr($key,1,2); #km
#/home/s0571283/positiveSet/pdb0704071050/pdb/km/pdb1kmc.ent
   my $pdbFile = $startDir . $dir . '/' . 'pdb' . $key . '.ent'; 

   open(PDBFILE, "<$pdbFile");

      while(my $line = <PDBFILE>){
         if($line =~ /^ATOM/){

            for my $index ( 0 .. $#{ $hash{$key} } ) {
#look for chain ID, eg: 'A'
               if( substr($line,21,1) eq $hash{$key}[$index]){
                  open(SINGLE, ">>$startDir".$dir.'/'."$key".'_'. "$ha
+sh{$key}[$index].pdb");
                     print SINGLE $line;
                  close(SINGLE);
               }
               if ($index !=  $#{ $hash{$key} }){
                  for (my $i = $index+1; $i < $#{$hash{$key}}; $i++){

                     if( substr($line,21,1) eq $hash{$key}[$index] || 
+substr($line,21,1) eq $hash{$key}[$i]){
                        open(DOUBLE, ">>$startDir" . $dir . '/' . $key
+ . '_' . $hash{$key}[$index] . "$hash{$key}[$i].pdb");
                           print DOUBLE $line;
                        close(DOUBLE);
                     }
                  }# for
               }# if($index !=  $#{ $hash{$key} })
            }# for my $index ( 0 .. $#{ $hash{$key} } )
         }# if($line =~ /^ATOM/)
   }#  while(my $line = <PDBFILE>)
   close(PDBFILE);
}# foreach
[download]

The crash happend when it was just printing a 'key'
foreach my $key (keys %hash){print "$key\n";
Could it be that I am running out of memory? I don't have much experience with scripts running for such a long time, can I monitor it (memory usage)?

Thanks a lot for your help so far!