Questions tagged [autodock]

Questions about the software AutoDock.

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1answer
91 views

How can I get Vina to recognise boron atoms?

I am trying to dock a ligand that features a boron (B) atom. AutoDock Vina throws an error with the following message: ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that ...
10
votes
1answer
168 views

Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?

I am not a chemist, but I know how to use AMDock to predict the binding affinity of a small molecule to a protein. There is a particular target for which AMDock Vina, with its default force fields, ...
4
votes
1answer
27 views

Procedure to validate glide docking without a reference ligand on Autodock vina

How can I perform a score-in-place procedure with autodock to validate ma glide docking? It is a new software for me and I don't Know how to use it and how to proceed. Thanks in advance for help.