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if ($_=~m/^ATOM\s+\d+\s+\w+\s+\w+\s+\w+\d+\s+(\S+)\s+(\S+)\s+(\S+)/){

open (IN, '6U9D.pdb.txt');

my $filename = '6U9D.pdb.txt';
open (IN, $filename)
    or die "Couldn't open '$filename': $!";

%amino_acid_conversion = (
    ALA=>'A',
...
    ILE=>'I',
    VAL=>'V'
);