| has a special meaning in a regex: it separates alternatives. If you know your variable should not contain any special characters, you can "quote" it by using \Q: 
my $id_to_match = '1QJ8:A|PDBID|CHAIN';
while (<>) {
    if (/\Q$id_to_match/) {
        # ...
    }
}

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See Escape sequences in perlre for details.

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: Question on REGEXP by choroba
in thread Question on REGEXP by Anonymous Monk

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