[gmx-users] Questions about GB parameters

[Justin A. Lemkul]

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

========================================