[Dock-fans] DOCK6.7 protein contain waters

Trent E. Balius tbalius at aol.com
Wed May 18 08:31:26 PDT 2016

 Hi Haiyang,

The best way to include water in your docking is to include them as part of your receptor.  

I would recommend using chimera to prepare your receptor.  
Remove all water except those that you want to include. 

Then do one of the following:
(1) You can  use the DockPrep tool be sure to deselect the "Delete solvent" option. 
(2) Or you could add hydrogen and charges and then save as a mol2 file yourself.

You can then give this mol2 file to DOCK's grid program.

Take care,



Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius



-----Original Message-----
From: 钟海洋 <zhonghy14 at lzu.edu.cn>
To: dock-fans <dock-fans at docking.org>
Sent: Wed, May 18, 2016 1:56 am
Subject: [Dock-fans] DOCK6.7 protein contain waters

Hi guys,

   I want to use the DOCK6.7 to perform docking proteins with waters, but I didn`t find the examples about that. Could DOCK6.7 dock 

proteins with waters?

                                                  Haiyang Zhong  
Dock-fans mailing list
Dock-fans at docking.org

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