[gmx-users] Partial charges correction from PRODRG

[Justin Lemkul]

On 10/26/16 6:20 AM, gozde ergin wrote:
> Dear all,
>
> Thanks to the Lemkul et.al. 2010 paper, we know that charges are often inconsistent in topologies produced by PRODRG.
> I have two types organic molecules to simulate, SDS and C12betaine.
> There are a lot of studies about SDS so I found the optimised charge distribution for Gromos-UA force field for SDS.
> However I struggle to optimise the C12betaine charges.
> Do you have any hint to optimise the C12betaine charges for Gromos-UA?
>

Recent versions of GROMOS96 have reparametrized choline headgroups, which could 
be a source of the initial charges and types for the quaternary amine.  The acid 
is a defined moiety, then the carbons in the tail all have zero charges.

-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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