AMBER Archive (2002)

Subject: Re: Solvent exposed surface area over a trajectory

From: Natasja Brooijmans (nbrooij_at_itsa.ucsf.edu)
Date: Thu Oct 17 2002 - 14:35:34 CDT

There are several diffferent programs available that can do this for the
complete surface, e.g. MSMS (developed in Sanner's group) or MOLSURF. You
will just need to write a simple csh script or perl script to loop over
differetn structures and average at the end, which you will have to
create. The MMPBSA script basically does this. If you're interested in
areas per residue, I would recommend SURFV or SUFVCV from the Honig lab.
You can choose to get the output per residue or per atom as well as the
full surface area. Most of these programs are freely available.

Hope this helps,

Natasja

Natasja Brooijmans
Graduate Program in Chemistry & Chemical Biology
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-0446
phone: 415-476 8291
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu

On Thu, 17 Oct 2002, Rebecca Perlow wrote:

> Dear AMBER users,
>
> I am wondering if anyone knows of a program that will calculate the
> solvent exposed surface are of a residue or group of atoms over a
> trajectory. I know that the Insight program calculates the value for a
> static structure, but I wanted to get this value over an entire
> trajectory.
>
> Thanks in advance for any suggestions.
>
> -Rebecca Perlow
>
> Rebecca A. Perlow, Ph.D.
> Department of Biology
> New York University
> 100 Washington Square East
> New York, NY 10003
> Tel: (212)998-8228
> E-mail: perlow_at_alum.mit.edu
>
>
>
>