Note that the SASA term is intended to account for the *difference* between
the hydrophobic effect and lack of solvent vdw interactions. Jason alluded
to this. So, simulations without SASA treatment are *not* lacking a
hydrophobic term, as is commonly suggested.
On Apr 9, 2012 12:27 PM, "Aron Broom" <broomsday.gmail.com> wrote:
> Thanks Jason, I think that is precisely the information I needed. I had
> two different simulations in mind, one in which I'm just trying to relax a
> protein structure a bit and gather some information on the folded ensemble,
> and another in which I was hoping to try and unfold the protein slowly. It
> seems from your answers as though for the first case gbsa=0 would be fine,
> whereas in the second case it might be good to go with gbsa=1, but probably
> something that will need some extensive testing.
>
> Thanks again,
>
> ~Aron
>
> On Mon, Apr 9, 2012 at 1:10 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Mon, Apr 9, 2012 at 12:15 PM, Aron Broom <broomsday.gmail.com> wrote:
> >
> > > Hi AMBER Users,
> > >
> > > In reading through the Generalized Born section of the manual, I see
> that
> > > the surface area calculations are off by default gbsa=0. Does this
> mean
> > > that there will be no penalty for exposing hydrophobics to the implicit
> > > solvent in this case?
> >
> >
> > I would claim that force fields are a little too complex to say yes or
> no.
> > Unravelling the protein will remove favorable VDW interactions between
> > hydrophobic regions for one thing (along with a myriad of other effects,
> of
> > course), which I would argue is a penalty for exposing hydrophobics.
> > Setting gbsa=0 will disable the surface area-specific terms which
> typically
> > serve to minimize SASA, but I've noticed that my simulations are quite
> > stable running in GB solvent without a nonpolar term (i.e., my
> simulations
> > have gbsa=0).
> >
> >
> > > If one is attempting to reconstruct the correct
> > > secondary structure or other structural features for a peptide, would
> > > gbsa=1 generally be the recommended setting?
> > >
> >
> > I think it's typically more important for methods like MM/GBSA where
> > solvent exposed regions change rather significantly (you're removing a
> > ligand from a bound site, after all) -- I haven't seen stability problems
> > with my GB simulations where I use gbsa=0. Furthermore, I don't think
> > gbsa=1 is nearly enough to correct GB when it performs badly for
> > conformational sampling, so for dynamics I think you may be fine omitting
> > it (it does depend on your study and system, though, and what you're
> trying
> > to learn).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> 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 Mon Apr 09 2012 - 13:00:03 PDT
