use strict;

my @superchunk; # i think i'm hyper enough as it is ...
my $i = 0;

open(IN,'output.txt') or die $!;

# process one line at a time
# add each line to the element that $i is
# increment $i when TIMESTEP is encountered
while (<IN>) {
   $superchunk[$i] .= $_;
   $i++ if /^TIMESTEP/; 
}

close IN;

$i = 1;

# process one element at a time
# use sprintf to create the name of the file
# write that element to the file
for (@superchunk) {
   my $file = sprintf("%s%02d%s",'BRO',$i++,'.pdb');
   open(OUT,">$file") or die "can't write to $file: $!";
   print OUT $_;
}