AMBER Archive (2008)

Subject: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber

From: John Chodera (jchodera_at_gmail.com)
Date: Mon Oct 27 2008 - 17:12:31 CDT

Hello all,

I have a question about how precisely improper torsions that are to be
applied to small molecules that have been parmeterized for GAFF by
antechamber are generated.

As far as I can tell, there are at least THREE programs that identify
all of the improper torsions in the AmberTools distribution:

* prepgen
* parmchk
* leap

The codebases for these three programs are entirely separate, and the
algorithms they use for identifying impropers appear to all be
different.

LEaP appears to have the 'final word', in that it actually searches
for torsion parameters to apply. There are anecdotal reports (on the
mailing list) of users finding that parmchk fails to generate all the
parameters expected by LEaP, which will still complain about missing
impropers until they are added to the gaff.dat file.

My question:

In converting small molecules over to Desmond, I need to identify all
of the improper torsion angles in the small molecule. Would running
'prepgen' (or some other antechamber-based tool) be sufficient to do
this, or should I run leap and examine the output if I want to
generate something that will be exactly the same as what would be
generated for Amber?

Many thanks,

- John 

-- 
John D. Chodera
QB3-Berkeley Fellow, University of California, Berkeley
email: jchodera_at_gmail.com
mobile: 415.867.7384
url: http://www.choderalab.org
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu