[Chimera-users] Docking

[Muhammad ALi]

Sir when I download a ligand from PDB site it contains may ligand molecules ..and kindly tell me how to get a single ligand????

--- On Thu, 4/11/13, Elaine Meng <meng at cgl.ucsf.edu> wrote:

From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Docking
To: "Muhammad ALi" <muh.ali741 at yahoo.com>
Cc: "chimera-users at cgl.ucsf.edu Mailing List" <chimera-users at cgl.ucsf.edu>
Date: Thursday, April 11, 2013, 4:24 PM

Hello,
The Chimera "AutoDock Vina" dialog has a choice: Executable location "Opal web service" or "Local."  To use Local, you would first need to download and install the AutoDock Vina program on your own computer, and then put the location of that executable in the Chimera dialog.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

AutoDock Vina is from a different group (it is not developed by the Chimera team).  You would have to go to the AutoDock Vina website to download the program, and to find more information about how that program works. 

AutoDock Vina website:
<http://vina.scripps.edu/>

AutoDock Vina paper:
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Trott O, Olson AJ. J Comput Chem. 2010 Jan 30;31(2):455-61.
<http://www.ncbi.nlm.nih.gov/pubmed/19499576>

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

On Apr 11, 2013, at 6:51 AM, Muhammad ALi wrote:

> Sir I am doing docking with autodock vina in Chimera.. but sir i successfully did it, but with Opal server, and found the required binding sites of ligand binding and checked theier bonds,, but kindly sir tell me  how can i do it without using opal server.. which file will be required???? and how it is estimated that which binding between ligand and protein is best and how???

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