[gmx-users] Adding missing heavy atoms
jalemkul at vt.edu
Mon Jul 27 02:12:57 CEST 2015
On 7/22/15 1:00 PM, prasun kumar wrote:
> Dear Justin and tarak
> Thanx alot for the reply
> If I have base atoms, so I have stacking information also.
> I was curious to know whether by changing the forcefield information will
> help me or not.
> For example, when I need ADNA, I will use some other information related to
> it and like that it continues for BDNA or ARNA
Any force field that needs to use conformation-specific parameters to enforce
some geometry is a bad force field. Thankfully, I know of no force fields that
do this. Proper force fields will correctly sample conformational fluctuations
that reflect the real ensemble of the biomolecule in solution.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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