On the face of it, your problem is easily solved with Perl. You just need a little help with the jargon. 

use strict;
use warnings;

[download]

...would show you that $m51 is not defined on line 39. This is probably a typo -- please use real code :D.

It is not clear what the script should be doing, other than rewriting all the ATOM lines, without field 4.

This snippet (reformatted for "standard" readability): 

foreach $line (@m3,@m5){
    if ($m3[$line] eq $m3[$line+1]) {
        $m5[i]=$m5[i+1];
    } elsif ($m3[$line] ne $m3[$line+1]) {
        $m5[i+1]=$m5[i]+1;
    }
}

[download]
...tries to index @m3 by using one of its values. According to your regex, $m3 is \w{3}, so it will probably evaluate to index 0. Also, using "i" as an index should not compile.

Please show us your sample script, and a sample input and output (what you got, and what you really want). We can then walk you through this.

-QM
--
Quantum Mechanics: The dreams stuff is made of

In reply to Re: Rearrange the residue number of a pdb file according to the residues names by QM
in thread Rearrange the residue number of a pdb file according to the residues names by nastaziales

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