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

[Justin A. Lemkul]

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.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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-- 
========================================

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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