Re: help about charmm

[Rick Venable <rvenable(at)pollux.cber.nih.gov>]

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
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 (301) 496-1905   Rick_Venable(at)nih.gov
 ALT email:  rvenable(at)speakeasy.org
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