Thank You Daniel,
I will try this up.
On Tue, Sep 28, 2010 at 9:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 22:00:03 PDT
