[gmx-users] OPLS/AA support for DNA

[Justin Lemkul]

On 3/25/15 8:02 PM, Alex wrote:
> I think I just googled my head off trying to find out if oplsaa supports
> DNA chains, and I just can't find a definitive answer. In a 2008 post,
> Justin suggested that AMBER is a better choice for DNA, but more recent
> posts indicate that people casually use oplsaa with DNA (at least that's my
> understanding).
> There are some reasons I'd like to stick with oplsaa with my project. Not
> set in stone, but highly desirable.
>
> Any ideas?
>

There are no nucleic acid residues in the OPLS .rtp file.  There are some 
parameters floating around the Web, but I question their reliability.  AMBER or 
CHARMM parameter sets are a much better bet here, especially the latest 
versions.  I don't know of any officially published OPLS nucleic acid parameters 
(if someone knows of any, please speak up, but my searches have turned up nothing).

-Justin

-- 
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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 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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