use File::Find;
$folder = '/usr28/users/mpcamp/ZDOCK/';

find (\&first, $folder);

sub first {

if ($_ =~ /com1/) {
print "Processing $File::Find::dir/$_ \n\n";


open (FILE1, "<com2");
open (FILE2, "<$_");
open (OUT, ">output");

while (($num1 = <FILE1>) && ($num2 = <FILE2>)) {

###do something