Ah, apologies here. I might have misread your original question. If you
are doing just energy analyses on single structures, PB is a better
starting place as Hai and Carlos stated. For MD, GB is the only realistic
choice (MD with PB is still a very active area of research as I understand
it, and getting stable forces is a challenge).
HTH,
Jason
On Fri, Mar 11, 2016 at 8:37 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 11 2016 - 18:00:09 PST
