In addition to what has been said, you could make the array variable "aminos" global, so that it can be accessed by all. But it's better to make a variable available close to where it's are needed.

Your values to your scalar variables maybe gotten from the CLI and checked if initialized.

Modifying your post a bit like this works, but you might still have to work on it or incorporate it with your code.

use warnings;
use strict;
use Getopt::Long qw(:config gnu_getopt);

help() if $ARGV[0] !~ /^--/;

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

GetOptions(
    'substr1=s' => \my $substr1,
    'substr2=s' => \my $substr2,
    'sub'       => \&a,
    'help|?'    => \&help,
);

sub a {

    if ( "$substr1$substr2" =~ /[^@aminos]/ ) {
        print "hello\n";
    }

    print "@aminos\n";
}

sub help { print "Usage: script --substr1 value --substr2 value --sub"
+; exit }
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You might have to check the usage of Getopt::Long again.

Note, I didn't check for the initialization of substr1 and 2