[gmx-users] filling missing param values

[Justin Lemkul]

On 7/25/13 8:25 AM, gromacs query wrote:
> Dear All,
>
> I am working on some molecule and I have defined atom types with OPLSaa and
> all atom types really exist in oplsaa and well chosen so no approximation
> in choosing atom types. During grompp, I found there are dihedral param
> missing. e.g.
> N CT CT NT
> N CT CT N3
>
> Is there any 'good' way of finding/assuming dihedral params for this? or I
> should choose values of some nearby atom types?
>

The OPLS dihedral fitting strategy is exceptionally well explained in the 
Kaminski 2001 paper (reference in Gromacs manual).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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