VMD-L Mailing List

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Sun Feb 24 2008 - 12:38:49 CST

Hi,

The binding site of my system is a shallow depression on the protein
surface. I'm trying to measure SASA to get a rough estimate of size of the
binding site. I read previous posts about the usage of "measure sasa", but
I'm still a bit confused, mostly the difference between using and not using
"-restrict" option.

Here's what I'm trying to do:

# select the atoms within 8A of the ligand
set binding_site [atomselect top "protein within 8 of ligand"]
set all [atomselect top protein]

measure sasa 1.4 $all -restrict $binding_site
measure sasa 1.4 $binding_site

The above two "measure sasa" lines return quite different SA values. Which
one is correct? What is the right way of estimating SA for a binding site?
Should I also include the atoms within selected residues, but outside 8A
cutoff?

Any help will be greatly appreciated!

Dong Xu