Sure. The easiest way, IMO, is to use the "surf" representation (or use the
MSMS plugin) in VMD.
On Fri, Oct 7, 2011 at 11:28 AM, kirtana S <skirtana4.gmail.com> wrote:
> Thank you for the information. Is there a way of representing the solvent
> accessible surface visually in graphics.
>
> Thanks
> Kirtana
>
> On Fri, Oct 7, 2011 at 8:34 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Thu, Oct 6, 2011 at 5:22 PM, kirtana S <skirtana4.gmail.com> wrote:
> > > Thanks for all suggestion. Can you tell how can I get solvent accesible
> > > surface area of selected residues .
> >
> > I'm not sure you can do that with sander. With cpptraj you can do this
> > by specifying a mask, so for example if you just want the SASA of
> > residues 5 to 10:
> >
> > surf :5-10 out surf.dat
> >
> > -Dan
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 07 2011 - 09:30:03 PDT
