ADL: How do you use the score_only parameter in vina?

Sami Marroun marroun.s at gmail.com
Mon Feb 10 07:15:10 PST 2014


Hello everyone,

I performed a rigid ligand docking using vina. The scores obtained in rigid
ligand docking are not directly comparable to those obtained by flexible
ligand docking.
Therefore, I want to use the score_only parameter in order to obtain
"flexible ligand like" scores. How is this done?
Can I use the output of the rigid docking (all 20 poses) and rescore them
directly or do I have to split my output file into 20 and basically run a
docking with score_only for each?
Furthermore, do I have to redefine rotatable bonds for a given output pose
(by running the prepare_ligand.py script or through ADT?

Sami,


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