Re: AMBER: Specific/Non-specific dihedral issue in Amber

From: David A. Case <>
Date: Tue, 17 Jul 2007 16:15:59 -0700

On Tue, Jul 17, 2007, Narayanan Veeraraghavan wrote:
> I'm sorry to drag this issue, but I still don't see the bottomline.
> >Same idea for specific vs. non-specific: if you put in specific parameters
> >for a torsion, you should include specific versions for all multiplicites
> >(even those that might have a zero force constant). Basically, don't leave
> >LEaP any choice about which set (general, specific, frcmod) of parameters
> >to use.
> The question remains, if there exists a specific dihedral with say
> multiplicity 1 and a generic dihedral with multiplicity 3, for e.g.
> H1-CT-CT-OS 1 0.25 180 1
> X -CT-CT-X 9 1.40 180 3
> should we include the generic dihedral with a multiplicity say 3, with
> the force constant as given in the generic dihedral definition, eg:
> H1-CT-CT-OS 9 1.40 180 3
> or with a zero force constant (which basically implies disregard the
> generic)?
> H1-CT-CT-OS 1 0.00 180 3
> Could you tell what *ought* to be the rule?

The "rule" is to do whatever matches the assumptions of the persons who
constructed the force field in the first place.

> BTW, the system is a nucleic acid (sugar) with parm99.dat ff.

The nucleic acid force field people should chime in here. I've almost always
used parm94 (not parm99). In particular, someone knowledgeable should check
to see if this problem arises with frcmod.parmbsc0.


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Received on Wed Jul 18 2007 - 06:07:53 PDT
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