Subject: timeseries for volume a macromolecule's cavity

From: Jerry Ebalunode <jebalunode.-at-.adrik.bchs.uh.edu>
Date: Fri, 20 Feb 2004 23:50:51 -0500

Hi all,
I would like to analyze the calculated the volume of a protein's cavity(s) 
buried or partially exposed as a function time  for an entire trajectory
data collected from molecular dynamics simulation. There are quite a few good 
tools available to calculate the volume for individual protein
conformations such as PASS or CASTp or CCP4's VOLUME utility. However these tools are
not practical for calculating 100's protein configuaration from MD data. Has
any one come across any programs  or toolkits that could be used for perfoming 
this task within a reasonable time. Thanks in advance for any suggestions
or help in solving this problem. 
-- 
Cheers,

Jerry Ebalunode
Graduate Research Assistant
RM 402F Houston Science Center
Phone: 713-743-8367
Dept. of Biology and Biochemistry
University of Houston
4800 Calhoun Road
Houston, TX 77204