The GBSA option will turn on SASA calculation. If you run MD with
GBSA=1 a non-polar solvation energy term will be calculated using the
surface area and the SURFTEN parameter, you can get the SASA from this
(ENP = SURFTEN * SASA, see manual for more details). If you already
have a MD trajectory and you want to calculate SASA from it you can
post-process the trajectory using the imin=5 option. Note that if you
post-process you can use GBSA=1 or GBSA=2 whereas if you run MD you
can only use GBSA=1.
-Dan
On Tue, Sep 28, 2010 at 5:52 AM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
> Hi All,
> I am interested in calculating the change in solvent accessible surface area
> during MD simulation for protein of my interest. Is there any option for the
> same in amber.?
>
> Hirdesh
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>
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Received on Tue Sep 28 2010 - 09:30:04 PDT
