[gmx-users] Question about Improper Dihedral of Charmm in gmx &, ParamChem

[Justin Lemkul]

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On 3/3/14, 11:03 PM, Tom wrote:
> Thanks Justin!
> The result about the improper dihedral angle from ParamChem does keep
> me very confused. For the molecule (C6H5-NH2), the one of N H H C should
> not have improper dihedral however the websever showes there is one.
>

Why shouldn't it?  In CHARMM, an aromatic amine is, in fact, assigned an 
improper around N.  It's the same way across the nucleic acid and CGenFF force 
fields.  I would encourage you to spend some more time reading the related 
literature if this is an unfamiliar concept.

-Justin

> If anyone has the experience of Charmm improper dihedral, please give a
> help. Thanks!
>
> Thom

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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