[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Darrell Koskinen darrellk at ece.ubc.ca
Sun Oct 25 22:22:36 CET 2009

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?


> Date: Mon, 19 Oct 2009 19:07:22 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
> 	ffoplsaa
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4ADC1E3A.8010502 at 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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