Re: [AMBER] Accessible surface area

From: Jason Swails <>
Date: Wed, 17 Oct 2012 09:53:36 -0400

On Wed, Oct 17, 2012 at 4:47 AM, Esam Tolba <> wrote:

> Dear all
> How can I use ptraj to measure the solvent accessible surface area for the
> protein? and also for each individual residue in the structure?
> *Best Regards,
> Esam
> *

You will need to use cpptraj. You can either use the molsurf or the surf
command to get the Connolly or LCPO surfaces, respectively.

You can specify a mask for which to calculate the surface, in which case
you will have to use a separate command for each residue, I think (but this
can be scripted).


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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Oct 17 2012 - 07:00:09 PDT
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