Carlos,
I'm slightly confused, does this mean that without the SASA term it would
actually be *harder* to expose a hydrophobic region to solvent because
there is no compensatory VDW term?
~Aron
On Mon, Apr 9, 2012 at 3:47 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > > _______________________________________________
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> > > 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
> >
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Apr 09 2012 - 16:30:03 PDT
