[gmx-users] orientation restraints in binding free energy calculation

[Chunxia Gao]

Dear gmx-users:

I read some research articles of calculating the binding free energy, still I can not figure out how to get the orientational parameters. 

If I have the crystal structure of ligand bound protein, so I need to choose three anchor atoms in the protein and three anchor atoms in the ligand respectively? 

How to define these three atoms in ligand and protein, can I choose them arbitrarily? and then define one distance, two angles and three torsions?

After I have the reference orientation, what should I do?

Millions of thanks for answering my questions.

Regards
Chunxia