open my $fh_in,  "<", $proteinfilename or die "Couldn't open '$proteinfilename': $!";
open my $fh_out, ">", $outfilename or die "Couldn't open '$outfilename': $!";

while (my $line = <$fh_in>) { 
    if ($line =~ /^AD/) {
        print $fh_out " $line";
    }
}