According to the below link:

https://www.schrodinger.com/kb/573

One can compute the binding affinity of a docked complex using PRIME MMGBSA and macromodel embrace.

My questions are:

1. There are two modes in which the Embrace calculation, that is, Energy difference mode and Interaction energy mode. Which mode should I employ?

2. If we use embrace macromodel, which of the following embrace descriptors do we use to rank the binding affinity of the ligands that is,

Embrace_Total_Energy_without_constraints

Embrace_Valence_Energy

Embrace_vdW_Energy

Embrace_Electrostatic_Energy

Embrace_Solvation_Energy

Embrace_Constraint_Energy

Thanks