On 6/23/16 7:17 AM, Anurag Dobhal wrote:
Dear Justin,
The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.
To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.
(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
please enlight me where I am going wrong.
I think you misunderstood what I said in that thread.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html
"You should find force field parameters specifically for the base from published
literature or from another force field."
This means: find a force field that has parametrized the species you need and
use it. This does not mean: hack together something from "any other force
field" you like and try to make it OPLS-AA. You did not say before that you
were dealing with a complex system like this. You just said your guanine
charges didn't add up. So I addressed that problem.
Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an
invalid approach.
Pick a force field. Use that force field. Do not try to kludge together some
hybrid entity. Force fields are designed to be internally self-consistent. If
you do not have a proper balance of interactions, you are not doing a useful
simulation. You are generating random numbers.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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