AMBER Archive (2002)

Subject: Re: Solvent exposed surface area over a trajectory

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Thu Oct 17 2002 - 14:09:17 CDT

you may want to look at molsurf. You could take snapshots of the
trajectory using the gc option in mm_pbsa and then analyze the sasa
using molsurf.

Just a guess, we'll see how the big guns weigh in on this question.

Michael Ford

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