ligand binds one site effects the other?

["Rowyna K." <nepenthes (+ at +) bigfoot.com>]

Dear all,
 I wonder if there is anybody who can help in my search for an answer. I work
 with a protein which
 binds to six ligands on six sites and I am wondering how I can find out if there
 is some cooperative
 effect when the ligands bind or not (computationally). Since the protein is kept
 rigid during
 docking precedure, I am left wondering how I might know if there are changes
 happening in the other
 sites.  I am hoping that if anybody who is working on something similar can
 share some knowledge and
 advise. I think by running MD, i might be able to find some answers but I have
 not started yet. I
 would like know if there are other ways or if I'm wrong, what is the correct
 method? Any reference
 to literature would be helpful as well.
 Thank you all for you time and sincerely hope somebody will be able to share
 their opinion.
 Regards,
 Rowyna K.