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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Apr 09 2012 - 10:30:05 PDT
