Per Larsson wrote:
Hi!
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.
-Justin
/Per
6 jul 2011 kl. 04:29 skrev "Justin A. Lemkul" <jalem...@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
-- ========================================
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
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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