#!/usr/bin/perl -w


$sasa_file= 'File1';
$pdbfile='File2';

# Remove the newline from the DNA filename


open (MYXFILE,$sasa_file);
open (PDBFILE, $pdbfile);

while (<MYXFILE>){

chomp;
@sa = split(/\t/,$_);

#print "$sa[0]    $sa[1]    $sa[2]\n";
#$res = substr $_, 0, 4;
#$res_no = substr $_, 4, 5;
#$atom =substr $_, 9, 3;

    while (<PDBFILE>){
    chomp; 

        $res = substr $_, 17, 3;
        $res_no = substr $_, 22, 4;
        $atom =substr $_, 13, 3;

        #print " $res $res_no $atom \n" ; # works fine
            
        if (( $sa[0]eq$res)&&($sa[1]==$res_no)&&($sa[2] eq $atom))
            {
                print "$_"; # does not print anything.
                
            }
    
            }



            }

close MYXFILE;
close PDBFILE;
[download]

Hi yads25,

Please use <code> tags to wrap the coding parts in your nodes.

Can you please show us your sample file, so that we can give solutions without assumption.

Prasad