[gmx-users] Questions about GB parameters

[Per Larsson]

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.

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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