I agree with Hai. Even our best GB models are very approximate, and
designed to be used when speed matters (like MD forces). For
post-processing and when fast derivatives aren't needed I usually turn to
PB first.
On Mar 11, 2016 8:24 PM, "Nhai" <nhai.qn.gmail.com> wrote:
> Just add a bit to Jason' reply.
>
> We have updated new nucleic acid parameters for igb8 in Ambertools 15,
> (have better performance.)
>
> But try with PB calculation first. Try with GB later if speed is important.
>
> Hai
>
> > On Mar 11, 2016, at 7:51 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> > On Fri, Mar 11, 2016 at 6:09 PM, Arati Paudyal <apsilwal123.gmail.com>
> > wrote:
> >
> >> Dear all,
> >>
> >> While running GBSA to calcualte free energy change of a protein
> complex, I
> >> am kind of confused on what I should be using for "igb". I looked at the
> >> manual and that was too "algorithmic" explanation for beginner user
> like me
> >> to understand. So, could you please suggest what "igb" value should I
> use
> >> for my purpose? I have a protein complex and I want to find the Delta G
> >> using PB/GBSA.
> >
> > For proteins and nucleic acids, igb=8 typically performs the best.
> >
> >
> >
> >>
> >> Also, what salt concentration do we pick for the salt conc? My guess is
> >> that we use similar salt concentration to that of experimental
> condition.
> >> Is this right??
> >
> > Yes. For large salt concentrations, the simple model used in the GB
> code
> > is a much poorer approximation, though (we're talking concentrations
> around
> > .5M and greater, I think).
> >
> > HTH,
> > Jason
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Received on Fri Mar 11 2016 - 18:00:04 PST
