Re: Code won't proceed after input.

[toolic]

Your while loop is an infinite loop because you never increment the $counter variable inside the loop.

See also Basic debugging checklist

UPDATE:

I would appreciate ALL the help you have.

You can use qw to cut down on some typing:

my @AAMatrix = qw( A C D E F G H I K L M N P Q R S T V W Y );

You can use map and Range Operators to cut down on some more typing:

my @AAOcc    = map { 0 } 1 .. 20;

[Athanasius]

my @AAOcc = map { 0 } 1 .. 20;

Or just:

my @AAOcc = (0) x 20;

:-)

[AnomalousMonk]

Or better yet IMHO:

>perl -wMstrict -le
"my @AAMatrix = qw( A C D E F G H I K L M N P Q R S T V W Y );
 ;;
 my @AAOcc = (0) x @AAMatrix;
 print qq{@AAOcc};
"
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

[space_monk]

I ran out of votes before getting to your comment, but I definitely approve as it solves a common mistake where manual sizing of multiple arrays is involved