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

##</code><code>##

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

##</code><code>##

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

##</code><code>##

%amino_acid_conversion = (
    ALA=>'A',
    TYR=>'Y',
    MET=>'M',
    LEU=>'L',
    CYS=>'C',
    GLY=>'G',
    ARG=>'R',
    ASN=>'N',
    ASP=>'D',
    GLN=>'Q',
    GLU=>'E',
    HIS=>'H',
    TRP=>'W',
    LYS=>'K',
    PHE=>'F',
    PRO=>'P',
    SER=>'S',
    THR=>'T',
    ILE=>'I',
    VAL=>'V'
);