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:
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,
Embrace_Total_Energy_without_constraints
Embrace_Valence_Energy
Embrace_vdW_Energy
Embrace_Electrostatic_Energy
Embrace_Solvation_Energy
Embrace_Constraint_Energy
Thanks