in reply to local and global variable problem
Why are you looping on the same @aminos array? This is a little bizzarre.
For troubleshooting purposes, before you get into your outer for loop, could you do something like:
use Data::Dumper; print Dumper(\@aminos);
... and then show us what the output is? I suspect you'll need to change the way you're accessing the @aminos array...
*My* tenacity goes to eleven...