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).
Thanks, that makes sense then. The code and .mdp settings indeed reflect this.
I've updated the git manual to accurately describe this.
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.
I look forward to it :)
-Justin
Cheers /Per
21 jun 2011 kl. 18.42 skrev Justin A. Lemkul:
Can anyone comment further on either of these issues?
-Justin
Mark Abraham wrote:
On 15/06/2011 4:24 AM, Justin A. Lemkul wrote:
Hi All,
I wanted to dig up an old discussion that hit the list a long time ago
because I'm now encountering some problems understanding the GB
settings myself. The discussion in question is here:
http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html
I wanted to post a couple of questions based on Per's response.
1. Based on that post, it seems to me that the value in the gbr column
should have a dielectric offset added to it during the GB calculations.
In the code, though (genborn.c, around line 484 in the latest
release-4-5-patches), it looks like the dielectric offset is
subtracted, not added. I guess the code is reversing the process,
going from GB radius back to vdW radius by subtracting the dielectric
offset? It seems, then, that the parameters in gbsa.itp should specify
GB radii, not vdW radii, though the manual says the gbr column is
"atomic van der Waals radii, which are used in computing the Born
radii." Is the opposite actually true?
It does look to me as though something is mis-sense here. The quantity
given in gb_dielectric_offset is always subtracted from a value that I
think is found in the gbr column of [implicit_genborn_parameters]. Mark
2. I am still unclear on the source of the HCT scaling factors. From
the reference cited in the manual, it would seem that scaling factors
are interaction-dependent, at least when H atoms are concerned. I also
cannot find any indication of where these values came from. None of
the values of Table 2 in the HCT reference match the contents of the
"hct" column. Again I wonder if I'm missing something obvious :)
Thanks for any insight!
-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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