my @files = qw(file01 file02 file03 file04 file05); 

my $carboxyl = 0; # you may want to start at 1 instead
for my $filename (@files) {
  open my $pdb, '>', "$filename.pdb";
  my ($p, $w);
  my $bx = 50; # Never used again ?
  my $by = 50; # Never used again ?
  my $bz = 50; # Never used again ?
  print  $pdb "\t%filename\n";
  printf $pdb "%5d\n", $atomcount;
  for my $p (1 .. $atomcount) { # Perl likes to help
     printf $pdb "%5d%-5s%5s%5d%8.3f%8.3f%8.3f\n", 1,$carboxyl,@atom[$p],$p,@x[$p],@y[$p],@z[$p];
  }
  $carboxyl++;
  printf $pdb "%10.5f%10.5f%10.5f\n",$bx,$by,$bz;
  close $pdb; 
}