Re: Generalized Born Solvent Question

From: Roy Fernando (
Date: Fri Aug 03 2012 - 14:07:26 CDT

Hi Aron,

Did you refer to "Solvent Accessible Surface Area" by SASA?

Can we do this measurement in NAMD, in GBIS? I am intrigued!

Is there any documentation about using SASA in GBIS?



On Mon, Jul 30, 2012 at 6:06 PM, Aron Broom <> wrote:

> Just as an FYI to anyone who has this same question and discovers this
> thread, Dr. David Case informs me that once the Generalized Born
> calculations have taken place, all of the atoms are effectively chargeless,
> since the electrostatic portion of the calculations are done, and
> therefore, it is safe to treat SASA equally for all of them.
> ~Aron
> On Thu, Jul 19, 2012 at 2:34 PM, Aron Broom <> wrote:
>> Hi Everyone,
>> I've asked before about the SASA term with GBIS simulations, but I'm
>> still slightly confused and have what I think is a rather quick question:
>> So I understand that in a GBIS simulation without SASA, the lack of
>> potential VDW interactions between water and say a hydrophobic sidechain,
>> means that the sidechain will tend to favour interacting with the protein,
>> thereby giving a partial hydrophobic effect. Moreover, when one adds in
>> the SASA term, the energy gradients tend to favour burial of exposed
>> surfaces, ideally, recapitulating in full the hydrophobic effect. What I
>> don't understand, is that in my reading of the articles presenting these
>> methods, I don't see anything about the polarity of the atoms being taken
>> into account for this SASA term. To me, this would suggest that a solvent
>> accessible polar group is just as unfavourable as a similarly exposed
>> hydrophobic group as far as SASA is concerned. Furthermore, because
>> enthalpic interactions between polar groups are stronger than between
>> hydrophobic groups, this would imply that if one ran a GBIS + SASA
>> simulation of a protein for long enough, you'd end up with a "native state"
>> in which the polar groups were all buried in the core.
>> There must be something critical I'm missing here?
>> ~Aron
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

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