[gmx-users] Carboxylate OPLS-AA parameters

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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