[gmx-users] Cyclohexane OPLS-AA topology

[Justin Lemkul]

On 6/30/15 5:43 AM, Simone Aureli wrote:
> Hi, I created a topology file for all-atom cyclohexane molecule with
> OPLS-AA force field and I need a little help. I assigned to the Carbon atom
> the function opls_157, while to the hydrogen the function opls_156. Are
> they correct according to your opinion?
>

There's a lot of redundancy in the OPLS atom types with respect to the nonbonded 
parameters.  Those types end up being the same as opls_135 and opls_140, which 
are probably more "conventional" in representing hydrocarbons.  See e.g. amino 
acid side chains.  Whether or not those work for cyclic species, well...you'll 
have to try them and see.

-Justin

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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