AMBER Archive (2002)

Subject: Re: Solvent exposed surface area over a trajectory

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Thu Oct 17 2002 - 14:18:56 CDT

You might consider using naccess. It is quite fast compared to some
programs, but you have to run it seperately on each PDB. Remember, though,
that the residue names should be changed back to the standard form (en HIS
instead of HIP, etc.) (This programs gives accessible surface areas at
residue as well as atom level.)

Hope this helps,
-Sanjeev

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.