[gmx-users] Questions about GB parameters

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 6 04:29:22 CEST 2011

Per Larsson wrote:
> Hi!
> I did some digging and think I can clarify at least the first question.
> Sorry for the confusion with regard to the earlier post. What is specified in
> the gbsa.itp file under the gbr column is indeed vdW-radii. These are used to
> compute Born radii, as the manual says. The dielectric offset is subtracted
> from the vdW radii, as this has been shown to improve the agreement between
> PB and GB calculations (see eg. the OBC-paper, Onufriev, Bashford and Case,
> Proteins, 55, 383-394).
> For the second question, I am a little confused myself now. The values found
> in the gbsa.itp-file are exactly those found in the Tinker package (in the
> ksolv.f-routine), which also cites the same reference. Hmm...I'll be back
> again for this one.

Have you uncovered anything?  I've tried contacting the Tinker developers but 
have received no response.  I found the routine (in Tinker's born.f) that 
utilizes the values, but I still have no idea where they come from or why 
they're fixed for a given atom type rather than a given pair.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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