[gmx-users] from amber to opls

[Justin Lemkul]

On 5/22/14, 5:19 PM, Rebeca García Fandiño wrote:
> Hi,
> I have done a simulation of an organic molecule (a cyclodextrin) using GAFF/AMBER parameters, and I would like to compare the results using another force-field (OPLS or CHARMM). Is there any direct way to go from the topology for AMBER to the topology for OPLS or CHARMM?

You can't simply translate one force field to another.  You need to derive a new 
topology that is consistent with the other force field.  For CHARMM, you can use 
the ParamChem server to derive parameters under CGenFF; the output topologies 
are generally very high quality, though some small empirical adjustments may be 
necessary, but the majority of the hard work is already done :)

-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 601
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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