From: Jason Swails <>
Date: Mon, 9 Apr 2012 13:10:30 -0400

On Mon, Apr 9, 2012 at 12:15 PM, Aron Broom <> 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).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Apr 09 2012 - 10:30:04 PDT
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