To answer a few more questions:
  1. while ((my $line = <INFILE>) && ($line !~ /SEQ.../)) (Removed as per tye's second comment. Just look below - it's better code anyways.)
  2. It's Perl, not PERL
  3. The regex match operator is =~. The regex not-match operator is !~. It's an atomic 2-character-long operator, not something like += or -=.
  4. Rewrite as such: 
    while (my $line = <INFILE>)
{
    # Do a match against the line, grabbing the number.
    my ($num) = $line =~ /SEQRES\s{2,5}(\d)\s/;

    # This means that the line didn't meet our requirements
    # as defined by the regex. So, go get the next line.
    # (I added this ... you may not want it, depending on
    # what else you're doing in the loop.)
    next unless defined $num;

    # If that number is 2, leave the while loop.
    last if $num == 2;

    # Don't chomp unless there's a possibility we'll use it.
    chomp $line;

    # If the number is 1, print it to two places.
    if ($num == 1)
    {
        print "$line\n";
        print OUTFILE "$line\n";
    }
}

    [download]
Make it obvious what the difference is between the two matches. I assigned the difference to $num, which was done via the capture mechanism of regexes. (Look for the parentheses.)

Update: Changed code per tye's comments.

------
We are the carpenters and bricklayers of the Information Age.

The idea is a little like C++ templates, except not quite so brain-meltingly complicated. -- TheDamian, Exegesis 6

Please remember that I'm crufty and crochety. All opinions are purely mine and all code is untested, unless otherwise specified.

In reply to Re: more than one condition to a while loop by dragonchild
in thread more than one condition to a while loop by anchorite

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