I hadn't thought of it that way... basically I am trying to do a virtual screening project. I know that there are a lot of software packages out there to do this but I wanted to learn this for myself down to the implementation level, among other aspects of my project.
I think I need to back off and ask a more 'general' question in another thread so I can understand what concepts pertain to my project. I suspect I might not even be able to use empirical scoring because there are few structures (pdb code 3IBK) actually available with bound complexes. Most likely going to be force fields, which I have a gazillion questions about.
Thanks for your patience, it really means a lot to me