You don't need the quotation marks or the square brackets:

if ( /^\w[\s]+\w/ and not /^A pdb file/ )
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But my guess is you're also trying to match full words separated by a space with the first pattern, so:

if ( /^\w+[\s]+\w+/ and not /^A pdb file/ )
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Thank you all so much for your help!!!

Update:I didn't notice my copy/paste malfunction right away. Here's the full answer.

The problem is, the square brackets create a character class: i.e., any of the characters in between them will match. Remove the square brackets (and perhaps the double quotation marks, if you do not wish to match them), and it should work:

Your first expression matches a single word character, followed by one or more spaces, followed by another single word character (plus zero or more arbitrary characters after that.) Your intent may have been to match words of any length, in which case you would want to use \w+ instead of just \w.

You can combine those two expressions:

#!/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
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Output:

This line contains A pdb file
No pdb file, trailing spaces
Two   words and more
Two   wordsonly
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Finally, it would be easier to help you if you provided some sample input and expected output; I'm guessing in most of these cases. Hopefully I got it right! See How do I post a question effectively? for some hints for the future.

my @list = ('A test line',
            'foo bar',
            'A pdb file that I have',
            'this other thing');

foreach my $item (@list) {
  if (substr($item, 0, 10) ne 'A pdb file') {
    print "$item\n";    # Or do whatever...
  }
}
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Re-read 'perlre' those square brackets don't mean what you think they mean. You want:

  and not /^\"A pdb file\"/
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Square brackets means 'one character from this set'.

OK, you have been told about square brackets that create a character class. Just a small additional point to clarify. I am just wondering if you really want the double quotes. If you want to match the string with the quotes, then leave them in your regex, but it you added the quotes because you thought that were necessary to quote the string in your program, then removes them, they are not necessary. (I hope this is clear.)

In brief, /foo/ will match the string foo as well as the string "foo", but the /"foo"/ regex will not match the foo string, but only a string containing "foo".

And there is no need to escape the double quotes with a backslash.