Dear Discovery Studio experts:

A customer wants to find a way to refine CDOCKER result with detailed interaction analysis.
The ligands are peptides or oligonucleotides.
Because of their shear length, they interact with residues outside of binding pocket (active site) of a protein,
and CDOCKER energy is not a reliable index for them.

I guess the Simulation > Analyze Trajectory > Analyze > Calculate Interaction Energy protocol might be an answer.
A binding pocket group should be defined first, either manually or following an algorithm.
Then change parent of each docked ligand structure under the protein,
define a ligand group with the structure.
Then you can run the protocol to get interaction energy. Problem seems solved.

The problem is that one should do all the task for each of docked conformation; 20 conformations by CDOCKER default.
Worse, they are testing some 10K of ligands. It is simply impossible to do the task manually.
I could change parent, define groups, and run the protocol with Discovery Studio script,
but I failed to find how to collect the interaction energy in a table.

Could you please give me some hints?