[gmx-users] OPLS/AA support for DNA

[Justin Lemkul]

On 3/26/15 6:10 PM, Alex wrote:
> Yeah, I agree with Justin, this is pretty half-baked. On the other hand, I
> am not after conformational changes, ds-DNA simulations, or things of that
> nature. The things I am interested in would be mostly affected by the
> partial charges and vdW parameters, and all of those seem to be from
> standard oplsaa.
>

Everything in force fields is interrelated, and nucleic acids are particularly 
prone to deficiencies in bonded parameters, as the backbone dynamics are highly 
correlated.  There's a reason why nucleic acid force fields (especially in the 
AMBER and CHARMM families) have undergone continual development for the better 
part of 20 years.

See, for instance, dx.doi.org/10.1021/jz500557y

-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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