[gmx-users] meaning of the parameters in gbsa.itp

[Justin Lemkul]

On 10/24/13 12:11 PM, Coco Mo wrote:
> Thanks Justin for the quick hint!
> So, only the last two columns are needed. Sorry for the stupid question,
> where can I obtain reliable values for the atomic van der waals radii? Is
> it I have to calculate from the original force field parameters, in my
> case, the opls?
>

Four of the atom types you cite are carbon.  Note how the radius values barely 
change between different carbon types.  I would first start by assigning the 
parameters from something chemically similar.  The fluorine atom is more tricky, 
not so much in assigning the radius, but in assigning the scaling factor. 
You'll have to look for advice not from the OPLS force field papers, but from 
the GBSA algorithm you will be using.

-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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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