[Chimera-users] Autodock Vina tool

[Elaine Meng]

Hello,
The “AutoDock Vina”  tool in Chimera only connects to an outside web service (not from our group) running that program.  The Autodock Vina code is not part of Chimera.  See the AutoDock Vina website and paper for information on how it works:

<http://vina.scripps.edu/>
<https://www.ncbi.nlm.nih.gov/pubmed/19499576>

I am not the expert on either one, but my guess is that AutoDock uses the Lamarckian algorithm but AutoDock Vina does not.  They are two different programs. 

See also this previous discussion on the limitations of the Vina tool in Chimera:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-May/015758.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 22, 2019, at 2:34 AM, temban billyhp <btemban at yahoo.com> wrote:
> 
> Hi
> Is the lamagian algorithm used in chimera as a sub tool 
> 
> Sent from Yahoo Mail on Android
> 
> On Wed, 22 May 2019 at 3:06 AM, Elaine Meng
> <meng at cgl.ucsf.edu> wrote:
> 
> On May 21, 2019, at 4:38 PM, temban billyhp <btemban at yahoo.com> wrote:
> > 
> > Hi
> > During the auto dock vina operation, when building the grid box. What is the unit of the dimensions. I will equally like to know how to find the grid spacing value. 
> > Best regards.
> 
> 
> Chimera questions should be sent to chimera-users at cgl.ucsf.edu (CC’d here).
> 
> The Autodock Vina tool in Chimera does not have a grid spacing setting.  It only has the box center and size, which are in X,Y,Z coordinates of your atomic structure.  Atomic structures are generally in Angstrom units.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> 
> Maybe there is a setting to control grid spacing if you downloaded and used the Autodock Vina program directly (not using the tool in Chimera) but I do not know.  You would have to look at the Autodock Vina website for that information.
> <http://vina.scripps.edu/>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
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