[gmx-users] question

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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