[gmx-users] OPLS/AA support for DNA

[Smith, Micholas D.]

Granted, the previous parameter set I referenced, I found in under 2 minutes of searching, there was a paper in 2001 (see below) that discusses OPLS parameters for nucleic acids. The authors of that paper may have some better idea of where to find newer versions.

J. Pranata; S. G. Wierschke; W. L. Jorgensen; "OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform", J. Am. Chem. Soc. 113 2810-2819 (1991).

OPLS-AA/L really should have DNA support, as OPLS is one of the primary force-fields used in the commercial MD packages, it just looks like you may need to shoot an email to Jorgensen for the details.

-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 Alex <nedomacho at gmail.com>
Sent: Thursday, March 26, 2015 8:41 PM
To: Justin Lemkul
Cc: gmx-users at gromacs.org
Subject: Re: [gmx-users] OPLS/AA support for DNA

Well, just because I am asking about Gromacs, doesn't mean I don't
know about them interactions, especially the ones as mathematically
simple as those in Gromacs... Having said that, I agree that the
chain flexibility is greatly affected by bonded parameter issues.

However, the particular simulation I have in mind (translocation of a
near-linear ssdna chain periodic in length) is not going to be
drastically affected in this case, i.e. the order of magnitude of the
desired phenomena wouldn't change. There will be some effects, of
course, but I will be very suprised if it's drastic. I just come from
solid-state systems and wish I had experience with Gromacs that's
beyond editconf-genbox-pdb2gmx-grompp.

Come to think of it, you'd set up my system in about an hour. Care to
collaborate? :)))

Alex


JL> 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.
>>

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

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

JL> -Justin

JL> --
JL> ==================================================

JL> Justin A. Lemkul, Ph.D.
JL> Ruth L. Kirschstein NRSA Postdoctoral Fellow

JL> Department of Pharmaceutical Sciences
JL> School of Pharmacy
JL> Health Sciences Facility II, Room 629
JL> University of Maryland, Baltimore
JL> 20 Penn St.
JL> Baltimore, MD 21201

JL> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
JL> http://mackerell.umaryland.edu/~jalemkul

JL> ==================================================



--
Best regards,
 Alex                            mailto:nedomacho at gmail.com

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