#count the files in my foreach loop (I'm in a foreach loop, 
#not shown, that loops through @files
 my $count = @files;
 my @count = (); # I'l explain what I want to do with this - Note 1.
 push (@count, $count);
 print $count;
 print "\n";

#now this is where I am creating my new files, getting data from the 
#files in the foreach loop

 my $pdb;
 open (my $pdb, '>', "$filename.pdb");
 my $p;
 my $w;
 my $title = "$filename";
 my $bx = 50.000;
 my $by = 50.000;
 my $bz = 50.000;
 printf $pdb "%s$title";
 printf $pdb "\n";
 printf $pdb ("%5d",$atomcount);
 printf $pdb "\n";
  for ($p=1; $p<=$atomcount; $p++) {
    my $carboxyl = "@count[$w]"; #here is all that I want to do-Note 2
    printf $pdb("%5d%-5s%5s%5d%8.3f%8.3f%8.3f",1,$carboxyl,@atom[$p],$p,@x[$p],@y[$p],@z[$p]);
    printf $pdb "\n";
  }
 printf $pdb("%10.5f%10.5f%10.5f",$bx,$by,$bz);
 printf $pdb "\n";
 close $pdb/;