[gmx-users] filling missing param values
jalemkul at vt.edu
Thu Jul 25 14:47:03 CEST 2013
On 7/25/13 8:41 AM, gromacs query wrote:
> Dear Justin,
> Thanks this paper is quite explained and requires much detailed study
> (sorry am escaping!)
> As I have these two params missing, is there any tool that can help me in
> this regard or may be some approximation method I may use?
It is very hard to assign dihedrals based on approximations, and they are
generally not very transferable. Bonds and angles are easier, but dihedrals are
quite complex and the types and charges on atoms i and l have a significant
impact on the parameters. Shortcuts here will probably lead to a bad topology.
Parameterization is a hard road that takes a lot of time, even for bonded
terms that you think may be simple.
> On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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
>>> 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 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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Justin A. Lemkul, Ph.D.
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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