AMBER Archive (2002)

Subject: Binding site volume/Sander MD

From: Jianhui Wu (wujih_at_BRI.NRC.CA)
Date: Fri Aug 30 2002 - 16:20:09 CDT

Dear Amber Users,

I have a Sander trajectory and would like to analyze the change of
binding site volume in the course of MD. It contains bound ligand.

(1) Is there any amber module can do this kind of calcuation?
I think the bound ligand can be extracted from the trajectory if
neccessary.

(2) If not, could you point me to some sofware which can do the binding
site volume calculation? It would be nice if it be runned by script for
thousands of snapshots from the trajectory.

Thanks a lot,

Jian Hui