ADL: Force-field used in AutoDock Vina

Oleg Trott trott at scripps.edu
Thu Oct 4 10:48:33 PDT 2012


On Tue, Sep 18, 2012 at 5:26 PM, Saba Ferdous <saba.bsbi154 at iiu.edu.pk> wrote:
> Dear Mahasin,
>
> 1. AutoDock Vina uses Amber force field.
> 2. For certain metals, you need to incorporate the force field by editing
> the source code.
> 3. Docking only happens with water free protein. You have not to include
> water crytals.
>

Vina doesn't use the Amber force field, actually. Its scoring function
resembles X-Score. It should be able to handle metals in a way similar
to X-Score. Please see the paper for details.

Whether to include the water molecules is up to you.

Best,
Oleg
-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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