If I want to compare the change of A’s affinity to B before and after the activation of A, could I perform docking between unactivated A and B as well as activated A and B and compare their haddock score?
Hmmm… remember docking scores are not equal to binding affinity…
Never tried something like that. But you could and take the results with a big grain of salt 
Also, for the output parameters (van der waal energy .etc) Where could I read methods about how they are calculated?