I suspect more important than the radius set that you use will be the
algorithm you use. For example, LCPO (the default used in sander) has the
advantage of yielding analytical gradients for use in dynamics, but its
theoretical underpinnings are more suspect than other algorithms, like the
ones pbsa offers or what's available in molsurf.
HTH,
Jason
On Fri, Nov 18, 2016 at 1:12 PM, Pengfei Li <ldsoar1990.gmail.com> wrote:
> Hi Dave,
>
> Thanks for the quick reply. We just want to calculate SASA (solvent
> accessible surface area) for the amide NH groups of protein backbone (no
> GBSA calculations are intended to be performed). We want to use this
> property to predict the hydrogen exchange rates of the protein backbone
> amide groups with solvent water molecules. For this kind of situation, are
> the bondi radii also suggested?
>
> Best regards,
> Pengfei
>
> > On Nov 18, 2016, at 12:01 PM, David A Case <david.case.rutgers.edu>
> wrote:
> >
> > On Fri, Nov 18, 2016, Pengfei Li wrote:
> >>
> >> I am doing some SASA calculations now. There are different GB atomic
> >> radii settings in LEaP. For only calculating SASA but not doing GB
> >> energy calculation, which set of GB atomic radii is best to use? Thanks!
> >
> > Everything depends on why you are doing SASA calculations, and what use
> you
> > intend to make of the results. Is this for the "SA" part of GBSA? Then
> we
> > almost always use the same radii as were used for the GB part.
> >
> > If you want "standard" SASA results (e.g. to be compatible with what most
> > people use), the bondi radii are probably the best.
> >
> > ....dac
> >
> >
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>
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Jason M. Swails
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Received on Fri Nov 18 2016 - 11:00:03 PST
