ADL: Force-field used in AutoDock Vina
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.
Oleg Trott, Ph.D. (Columbia University)
Staff Scientist in the Olson Lab
The Scripps Research Institute
More information about the autodock