jalemkul at vt.edu
Sat Sep 12 21:29:19 CEST 2015
On 9/12/15 3:02 PM, Atila Petrosian wrote:
> Dear all
> Which force field is the best for simulation of RNA?
> - AMBER99
> - AMBER99SB
> - AMBER99SB-ILDN
There are no differences between any of these force fields with respect to RNA.
There have been many RNA-specific adjustments made to AMBER RNA parameters to
improve its structural and dynamical properties, though I do not know if any of
them have made it into GROMACS format yet. The most recent AMBER14 force field
is probably the best bet.
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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