in reply to Code won't proceed after input.

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 );

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

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

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Re^2: Code won't proceed after input.
by Athanasius (Archbishop) on Jan 23, 2013 at 16:06 UTC
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      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

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        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
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