It appears that you are intending to read through the file once for each protein in @acnumbers. You may be better off opening PFAMDB inside of your foreach $acnumbers... loop, or doing a seek to the beginning of the file prior to the inner foreach loop.

The way it is currently written, PFAMDB is being read once to the end of file, where it remains for every other protein in @acnumbers.

You may also want to explore BioPerl if you have not already.