According to the below link:
One can compute the binding affinity of a docked complex using PRIME MMGBSA and macromodel embrace.
My questions are:
There are two modes in which the Embrace calculation, that is, Energy difference mode and Interaction energy mode. Which mode should I employ?
If we use embrace macromodel, which of the following embrace descriptors do we use to rank the binding affinity of the ligands that is,