[gmx-users] OPLS/AA support for DNA

[Smith, Micholas D.]

There was some work on OPLS-AA/L on nucleic acids back in version 3 of GROMACS. The group that did the work has a website where they discuss the nucleic parameters located at: 

http://rnp-group.genebee.msu.su/3d/ff.htm

There are likely newer parameters out there for opls, but I haven't looked very hard for them.

Best of luck,

Micholas

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Wednesday, March 25, 2015 8:19 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] OPLS/AA support for DNA

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

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

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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