[gmx-users] Carboxylate OPLS-AA parameters
jalemkul at vt.edu
Sat Jan 25 20:37:12 CET 2014
On 1/25/14, 2:26 PM, rankinb wrote:
> Thanks for that information. The problem I am encountering is that the sum
> of the charges of the carboxylate ion are not summing to -1. Below is a
> list of OPLS-AA parameters, including a description of the atom type and
> charge. Assume I am trying to make a topology file for butanoate. The
> number of each atom is specified, as well as the total charge for each type
> of atom. The charge on the terminal methyl group adds up to -0.1 and the
> charge of the COO- head group is -0.9. Thus, if this is correct, the charge
> on the CH2 groups would need to add up to 0. I think the problem may be
> that I am using the wrong parameters of the hydrogen atoms (alkane H). Does
> anyone have any suggestions as to where I am going wrong?
> charge description number tot. charge
> opls 140 0.060 alkane H 7 0.420
> opls 271 0.700 C in COO- 1 0.700
> opls 272 -0.800 O in COO- 2 -1.600
> opls 273 -0.280 C in CH3 1 -0.280
> opls 274 -0.220 C in CH2 2 -0.440
Where are you getting these charges? I would suggest modeling your compound
after Asp or Glu. Alkane charges in OPLS-AA are rather formulaic, which is the
nice part about force fields that were parametrized using simple building blocks.
Justin A. Lemkul, Ph.D.
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
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