You are re-using too many variables, $lastchain in particular. 

$found = 0;
while ($line=<INFILE>) 
{
   chomp $line;
   if ($line=~/^COMPND[\s]{3}3/) 
   {
       $found = 1;
       # other processing here;
   }
}
$lastchain = '@' unless $found;

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--Bob Niederman, http://bob-n.com

All code given here is UNTESTED unless otherwise stated.

In reply to Re: otherwise condition by bobn
in thread otherwise condition by anchorite

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