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

Oleg Trott trott at scripps.edu
Mon Feb 10 16:27:16 PST 2014


Hi

"Scoring (only)" is done exactly as you would do regular docking
(which normally already uses a flexible ligand), except

a. you add "--score_only" to your options
b. the search space parameters can be omitted

Based on your question though, I strongly advise you not to use
"score_only". This is advanced functionality intended for very
experienced Vina users who can interpret the results critically.


On Mon, Feb 10, 2014 at 7:15 AM, Sami Marroun <marroun.s at gmail.com> wrote:
> 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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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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