Nidhi,
You might be interested in this tool: http://prody.csb.pitt.edu/drugui/
Here are slide from a talk about the method:
http://mmbios.org/images/workshops/HandsOn2014/Lecture3.pdf
And here is a tutorial:
http://prody.csb.pitt.edu/tutorials/drugui_tutorial/drugui_tutorial.pdf
I am sure that yo
Albert, I would love to, but I can't take time away from my work to do it,
unfortunately. I'm not one of the devs on the project - I've just talked
with them and played around with the tool while I was at PSC. You could
always write them, or just bite the bullet and run a few simulations in
NAMD :)