I managed to solve it

#!/usr/bin/perl
use warnings;
no warnings 'uninitialized';
#Calculating Protein Mass

($input) = $ARGV[0];
open ($in, "<", $input) || die "Can't open \"$input\".\nError = $!.\n"
+;

$protein = <$in>;
my(%mass_values) = (
  'A' => '71.03711 ', 'C' => '103.00919 ', 'D' => '115.02694 ',
  'E' => '129.04259 ', 'F' => '147.06841 ', 'G' => '57.02146 ',
  'H' => '137.05891 ', 'I' => '113.08406 ', 'K' => '128.09496 ',
  'L' => '113.08406 ', 'M' => '131.04049 ', 'N' => '114.04293 ',
  'P' => '97.05276 ', 'Q' => '128.05858 ', 'R' => '156.10111 ',
  'S' => '87.03203 ', 'T' => '101.04768 ', 'V' => '99.06841 ',
  'W' => '186.07931 ', 'Y' => '163.06333 ',
);

for(my $i=0;$i<length($protein);$i+=1) {
  $codon = substr($protein,$i,1);
  $mass = $mass_values{$codon};
  $sum += $mass;
}

print $sum;

($result) = $ARGV[1];
open ($out, ">", $result) || die "Can't write to \"$result\".\nError =
+ $!.\n";
print $out "$sum";
close "$out";

exit;
[download]

Just changed things some things, then it worked. Don't really know why. Still appreciate input / alternative methods