On Tue, Aug 20, 2013 at 4:27 AM, fatahiya <fatahiyamohdtap.yahoo.com> wrote:
> Hi all
>
> I'm running MD with implicit solvent method. Then, is it possible for me
> to calculate SASA?
>
Yes.
Not knowing what you _actually_ want to do (e.g., postprocess a trajectory
to compute the SASA of each frame? add a non-polar solvation term based on
the SASA to the force evaluation? which SASA algorithm you want to use?), I
can give no better answer. It is likely that you will be able to answer
your own question if you peruse the AmberTools manual (specifically the
cpptraj section) and Amber manual (the section about GB).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 20 2013 - 06:30:03 PDT
