We are trying to compare two possible docking sites between partners A and B. The problem is that we are unsure on how to compare the scores.
If we prepack the two sites independently using exactly the same structures for A and B but a different relative orientation, and using the same random_seed, even the minimized_away entry in the fasc file have quite different scores. So, how to compare the scores from two perturbation runs on the two sites ? By looking at the difference between the score and the energy of the minimized_away on the two sites ? (we think this could represent the interaction energy)
Another option we thought of, is to prepack one orientation, take the .ppk.pdb and manually reorient the two partners as in the second site.
Any suggestion ?