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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