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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Received on Mon Apr 09 2012 - 10:30:04 PDT
