I hope this helps.

#!/usr/bin/perl -w

use strict;
use warnings;

my %MWs;

%MWs = ( "A" => 71.1,
         "D" => 115.0,
         "F" => 147.1,
         "H" => 137.1,
         "K" => 128.1,
         "M" => 131.1,
         "P" => 97.1,
         "R" => 156.1,
         "T" => 101.1,
         "W" => 186.2,
         "C" => 103.1,
         "E" => 129.1,
         "G" => 57.1,
         "I" => 113.1,
         "L" => 113.1,
         "N" => 114.1,
         "Q" => 128.1,
         "S" => 87.1,
         "V" => 99.1,
         "Y" => 163.1,
         "\n" => 0.0 );

my $sum = 0.0;

print "Type amino acids.\n";

while ( my $line = <STDIN> ) {
  chomp $line;
  last if $line eq '';
  my @AA = split '', $line;
  foreach my $AA (@AA) {
    unless (defined $MWs{$AA}) {
      print "'$AA' does not exist\n";
      next;
    }
    $sum += $MWs{$AA};
  }
}

print "Molecular weight of this peptide is: $sum \n";
[download]

Hi mgbioinfo,

Have you printed out your variables at various points during the script to see that they contain what you think? Like:

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

...

while ( my $line = <STDIN> ) { # No need to declare $line until here.
    my @AA = $line;            # No need to declare @AA until here. 
                               # Might need to split the line, though 
+...

    print Dumper \@AA; # See what's really in that array. Note the bac
+kslash.

    ...
[download]

Later, in your loop, you pull an element from your array, but when you try to use it as the hash key, your syntax is wrong. Change:

foreach $AA(@AA) 
{
#I want now the sum of protein's molecular weight.
$sum += $MWs{ "$AA(@AA)" };
             # ^^
             # incorrect syntax
}
[download]

# Sum the proteins' molecular weights.
my $sum;  # no need to declare $sum until here.
          # Also no need to initialize to zero; Perl will do that when
+ you add to it.
foreach my $AA ( @AA ) {
    print "AA: $AA Weight: $MWs{ $AA }\n";
    $sum += $MWs{ $AA };
}
[download]

Hope this helps!

This code has more than a few problems. It's important to "keep your eye on the ball", so to speak, when programming. I use that term to stand in for the process of knowing where your data is, what it looks like, what variables hold what at each point while progressing through the code. The code above sort of takes guesses at what might be happening. For one thing, what do you think "$AA(@AA)" contains (you can print it to find out, and it will surprise you).

Here's one way to do it that will work for inputs that have a combination of upper case and lower case amino acids.

#!/usr/bin/env perl

use strict;
use warnings;

my %MWs;

#create the hash MWs with the amino acids and their molecular weight.

%MWs = (
    "A" => 71.1,    "D" => 115.0,    "F" => 146.1,    "H" => 137.1,
    "K" => 128.1,   "M" => 131.1,    "P" => 97.1,     "R" => 156.1,
    "T" => 101.1,   "W" => 186.2,    "C" => 103.1,    "E" => 129.1,
    "G" => 57.1,    "I" => 113.1,    "L" => 113.1,    "N" => 114.1,
    "Q" => 128.1,   "S" => 87.1,     "V" => 99.1,     "Y" => 163.1,
);

my $sum = 0.0;

print "Type amino acids. Hit [ctrl]-D when done.\n";

while ( my $line = <STDIN> ){
    chomp $line;
    next unless length $line;
    $sum += $MWs{$_} foreach
        grep {exists $MWs{$_}}
        map  {uc}
        split //, $line;
}

print "Molecular weight of this peptide is: $sum \n"
[download]

Hello mbgbioinfo,

$sum += $MWs{ "$AA(@AA)" };

$sum += $MWs{ $AA };