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

Mark Abraham Mark.Abraham at anu.edu.au
Sun Oct 25 22:47:14 CET 2009

Justin A. Lemkul wrote:
> 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.

I think you're both partly wrong. Type 140 is not for C-H in an aromatic 
ring, and if you grep 1.008 ffoplsaanb.itp you get many more H atom 
types with LJ. Certainly Justin's right inasmuch as amide N-H type 241 
has no H LJ parameters. Perhaps there's other text that Darrell hasn't 
found yet, or backbone nitrogen is not considered a heteroatom :-).


>> 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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