From: Aron Broom <broomsday.gmail.com>
Date: Mon, 9 Apr 2012 12:15:55 -0400

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? 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?



Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Apr 09 2012 - 09:30:06 PDT
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