RE: How to calculate free energy for conformational change

From: gaurav bhatti (gaurav15984_at_hotmail.com)
Date: Thu Jul 30 2009 - 23:51:05 CDT

Hi

I want to use steered molecular dynamics to pull two domains of a
protein apart from each other. I plan to do in by constraining domain 1
and applying a constant velocity to the domain 2. I know that I can
constrain domain 1 by setting the B or Occupancy column of these atoms
as 1 and using that as reference for constraints. Also I think I can
select the SMD atoms in the same way. My problem is with the direction
of pulling. I can calculate the center of masses of the two domains and
then apply velocity along the direction : COM2 - COM1. Is this a good
strategy?

Gaurav Bhatti

_________________________________________________________________
Missed any of the IPL matches ? Catch a recap of all the action on MSN Videos
http://msnvideos.in/iplt20/msnvideoplayer.aspx

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:17 CST