#!/usr/bin/env perl

use 5.012;
use warnings;

print for grep { /^(?!A pdb file)\w+\s+\w+/ } <DATA>;

__DATA__
A pdb file is on this line
This line contains A pdb file
    A pdb file is indented too far
A pdb file, but trailing spaces are here
No pdb file, trailing spaces
Two   words and more
Two   wordsonly

##</code><code>##

This line contains A pdb file
No pdb file, trailing spaces
Two   words and more
Two   wordsonly