On Mon, Dec 6, 2010 at 10:36 AM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
> Dear Amber Community,
>
> Greetings.
>
> I want to calculate SASA of a protein, per residue basis. I tried molsurf,
> but
> it just gives
> the total SASA. Is it possible to calculate SASA per residue? also is it
>
I believe that mm_pbsa.pl, via the decomp functionality, can do this, but
I'm not sure. You can look through the mm_pbsa source to see if it does.
In any case, you can have sander calculate the per-residue SASA by setting
surften=1.0, idecomp=1 or 2 (see the manual for discussions of these
variables). This assures that the surface area will be multiplied by 1, so
it won't be changed (surften), and idecomp = 1 or 2 decomposes the
contributions in a per-residue fashion. MMPBSA.py will create mdin files
for you, if you use the -create-mdins flag. Alternatively, you can look at
utils.py, which should show you the input files that are actually created.
(You'll need to get the latest version on
ambermd.org/tutorials/advanced/tutorial3/py_script/ to get the decomp
functionality).
> possible to get polar and non-polar
> SASA separately ?
>
No.
Good luck!
Jason
>
> Thanks,
>
> Senthil Natesan
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Dec 06 2010 - 09:30:08 PST
