[gmx-users] Questions about GB parameters
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 6 14:02:09 CEST 2011
Per Larsson wrote:
> Yes, I did! Had to look up a conversation between me and the Tinker
> developers about precisely this.
> The values are indeed not the original ones, but rather developed internally
> by Tinker people so to minimise differences between analytical surface areas
> and GB, given the HCT-algorithm and using per-atom rather than per-pair scale
> factors. The values have not been published anywhere as such but "have been
> used by others and seem fairly robust", according to Tinker developers.
> In the light of all other approximations introduced with implicit solvent,
> the differences in results should be minor.
> Of course this needs to be properly documented, and it was very good that
> some light was shed on this.
Great, thanks for clarifying all of this! I will make a note to adjust the
documentation. At the moment, it sounds as if one should expect the exact HCT
pairwise scaling method, which is obviously not the case.
> 6 jul 2011 kl. 04:29 skrev "Justin A. Lemkul" <jalemkul at vt.edu>:
>> 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 MILES-IGERT Trainee
>> Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu
>> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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