my $stem = $ARGV[0];
my $start = $ARGV[1];
my $dir = $ARGV[2];

print "STEM: $stem\n";
print "START: $start\n";
print "DIR: $dir\n";

my $outstring;
while(<*.pdb*>){
    if(m,\.viols,){next}
    if(m,$stem,){
        chomp;               
        $outstring = $dir.$start.'.pdb';
        print `cp $_ $outstring\n`;
        $start++}}


##</code><code>##

Subroutine bits redefined at /System/Library/Perl/5.8.6/strict.pm line 11.
Subroutine import redefined at /System/Library/Perl/5.8.6/strict.pm line 27.
Subroutine unimport redefined at /System/Library/Perl/5.8.6/strict.pm line 32.
Use of uninitialized value in concatenation (.) or string at rename4lib.pl line 16.