AMBER Archive (2006)

Subject: Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why

From: David A. Case (case_at_scripps.edu)
Date: Wed May 10 2006 - 15:12:52 CDT

On Wed, May 10, 2006, Kenley Barrett wrote:

> Thank you very much for your reply--I really appreciate you taking the time
> to give me your advice. As you suggested, I looked at differences between my
> prep file and the prep files of all_amino03.in. I found a difference that
> seems to be the culprit: as the first line of all_amino03.in, it has the
> sequence: "1 1 2". The first line of my prep file had the sequence
> "0 0 2". When I changed it to "1 1 2", the prep file was then able
> to create a library file that didn't have the missing residue name.

The "0 0 2" should be fine. Can you say *exactly* what syntax you are using
in LEaP? i.e. when you say "the prep file was then able to create a library
file", what commands are you using?

This works for me:

   cd $AMBERHOME/test/antechamber/tp
   tleap -s
      loadAmberPrep tp.prepin.save
      saveOff TP test.off
      quit

Note that the "tp.prepin.save" file has "0 0 2" at the top. And the
"test.off" file above has the correct name in the entry.TP.unit.residues
table.

...dac
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