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
}
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To this:

# 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!