Re: [AMBER] questions on molsurf program

From: Jason Swails <>
Date: Mon, 6 Dec 2010 12:29:07 -0500

On Mon, Dec 6, 2010 at 10:36 AM, Senthil Natesan <>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, 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. will create mdin files
for you, if you use the -create-mdins flag. Alternatively, you can look at, which should show you the input files that are actually created.
(You'll need to get the latest version on to get the decomp

> possible to get polar and non-polar
> SASA separately ?


Good luck!

> Thanks,
> Senthil Natesan
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Dec 06 2010 - 09:30:08 PST
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