If I replace the get_file sub with:

sub get_file {    #to read from a file
    return <<SEQUENCE;            #return the string sequence

SEQUENCE
}
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I get:

Reading a file...
Use of uninitialized value $record_type in hash element at noname1.pl 
+line 53.
Parsing a file...
Getting data...
Use of uninitialized value $record_type in hash element at noname1.pl 
+line 59.
Use of uninitialized value $seqres in split at noname1.pl line 194.
Use of uninitialized value $lastchain in hash element at noname1.pl li
+ne 222.
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which is consistent with all those replies saying you need to handle blank lines.

Adding:

        next if $line !~ /\S/;
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as the first line of the for loop in parse_pdb_file cleans up 1/2 the warnings. Adding:

    return if ! defined $seqres || $seqres !~ /\S/;
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as the second code line of extractSEQRES fixes the rest. A better analysis of the code than I have done may suggest better places to detect and handle unexpected file content.