Subject: Re: help about charmm

From: Rick Venable <rvenable(at)pollux.cber.nih.gov>
Date: Thu, 26 Jun 2003 17:03:05 -0400

On Thu, 26 Jun 2003, wei wrote:
> I have a general question about charmm parameter file. for many
> dihedral angles there are multiple terms for their potential function.
> do I have to comment all the redundant terms before I do the
> simulation?

Definitely not.  In most cases, the multiple terms have different
periodicity, and represent several cosine functions being added together
to best fit results from QM calculations on model compounds for the
torsion in question.

There is also multiplicity at branching points; for example, the chi1
sidechain torsion for many amino acids would have energy terms for both
the N-CA-CB-CG torsion, as well as the C-CA-CB-CG torsion.  This has
been accounted for in the parameter development.

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable(at)nih.gov
ALT email:  rvenable(at)speakeasy.org
-------------------------------------
"Don't blame me, I voted for Kang."
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