Darrell Koskinen wrote:
I looked through the ffoplsaanb.itp file and see that all the H atoms
except for the following four have zero LJ parameters:
HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine & Guanine H-C2
However, in the paper "Development and Testing of the OPLS All-Atom
Force Field on Conformational Energetics and Properties of Organic
Liquids", it states: "The original OPLS (optimized potentials for liquid
simulations) potential functions used a partially united-atom (UA)
model; sites for nonbonded interactions are placed on all nonhydrogen
atoms and on hydrogens attached to heteroatoms or carbons in aromatic
rings". Later, the paper indicates that the paramters were adopted as
much as possible from the OPLS-UA force field. Thus, since "sites for
nonbonded interactions are placed on hydrogens attached to heteroatoms
", it appears to me that a site for a non-bonded interaction should
exist on the H atoms within ammonia. Is my interpretation incorrect?
I don't think so. Each of the above examples you've cited above is for a C-H
bond in an aromatic ring. In OPLS, all N-H bonds involved hydrogen atoms with
zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or
amine (LYS/LYSH), etc and you will see the atom types used.
-Justin
Thanks.
Darrell
Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4adc1e3a.8010...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi,
I see that the Lennard Jones parameters for the N & H atoms in
ammonia, represented by opls_127 and opls_128 in the file
ffoplsaanb.itp are:
opls_127 NT 7 14.00670 -1.020 A 3.42000e-01
7.11280e-01
opls_128 H 1 1.00800 0.340 A 0.00000e+00
0.00000e+00
Why are sigma and epsilon both zero for H? Are the LJ parameters for
H embedded in the parameter for NT? If so, how were these parameters
combined?
What do other H have? What do the OPLS-AA paper(s) have to say about
such H atoms?
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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