[gmx-users] Questions about GB parameters
per.larsson at sbc.su.se
Wed Jul 6 10:46:42 CEST 2011
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.
6 jul 2011 kl. 04:29 skrev "Justin A. Lemkul" <jalemkul at vt.edu>:
> Per Larsson wrote:
>> 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
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