[gmx-users] binding sites with MD

[Tom Dodson]

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 you could use GROMACS to do the simulated annealing step
instead of NAMD.

Tom