[gmx-users] Carboxylate OPLS-AA parameters

[Justin Lemkul]

On 1/26/14, 2:50 PM, rankinb wrote:
> After looking at the parameters used for Asp and Glu, I have found that those
> are the ones I identified to use for my simulations of carboxylates.
> However, there is no terminal methyl group on Asp or Glu, like there is on a
> linear carboxylate.  So, do you think it would be acceptable to use a
> terminal C atom, head group carbon atom, and head group oxygen atoms that
> are specific for carboxylates, but use carbon and hydrogen atoms for the CH2
> groups that were developed for alcohols?
>
> I don't see any other way to do this such that the total charge will be -1.
>

I would treat the methyl (opls_135, charge -0.18) and methylene (opls_136, 
charge -0.12) groups like any other aliphatic group.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
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

==================================================