[Dock-fans] auto-DUD-e and explicit water -- Dock 6.7

Trent E. Balius tbalius at aol.com
Wed Mar 23 09:06:25 PDT 2016

 Hi Jonathan,

  A subset of the systems of the DUDE systems are distributed with SB2010/SB2012 
  which are prepared for DOCK6  
  Otherwise, you will need to prepare the receptors yourself, 
  I would suggest using Chimera and its dock prep tool to help you prepare the receptors.
  I would also suggest using the mol2 file distributed with DUDE (audoDUDE is for DOCK3.7):   
     here are the mol2 files:
  Including waters is possible in DOCK3.7 but a little tricky: 
  see the following:
  you will need to use "blastermaster.py -v --addNOhydrogensflag"

  For dock6 it is a little easier,  you just need to make sure that the water
  is in the mol2 file (and it has the right partial charges and atom type for grid to run properly).  

I hope that this helps,



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



-----Original Message-----
From: Jonathan Gough <jonathan.d.gough at gmail.com>
To: Dwight McGee <dwight.mcgee at gmail.com>
Cc: dock-fans <dock-fans at docking.org>
Sent: Wed, Mar 23, 2016 7:28 am
Subject: Re: [Dock-fans] auto-DUD-e and explicit water -- Dock 6.7

Hi Dwight,

Not exactly. At the moment, I am simply trying to reproduce the docking experiment for pygm. This is one of a few receptors in DUD-e that has an explicit water present in the receptor.pdb. 


In general, we are looking at explicit waters and water structure and would like to be able to use dock to run experiments with an explicit water (hence trying to reproduce pygm to make sure we know what we are doing).

Any insight would be appreciated,

On Wed, Mar 23, 2016 at 10:16 AM, Dwight McGee <dwight.mcgee at gmail.com> wrote:

Hi Jonathan,

Pertaining to question #2. Are you trying to identify ligands that make a specific water mediated interaction with the receptor?



On Tue, Mar 22, 2016 at 7:17 PM, Jonathan Gough <jonathan.d.gough at gmail.com> wrote:

Hi all,

2 questions - 

1. I was wondering if it is possible to use the files for auto-DUD-E in testing for Dock 6.7. It seems as if everything is set up for 3.7, but not for 6.7.  

Related to that, I tried using basic steps in the tutorials to reproduce the binding of the x-ray crystal ligand from pygm (in the DUD-E) using the ligand.mol2 and the receptor.pdb from http://dude.docking.org/ 

unfortunately, the generated poses were very far from expected. 

2. when prepping the grid scoring function (or the pdb/mol2), is there something special that I need to do to ensure that the explicit water is treated correctly or to make sure that the water parameters are included? 


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T. Dwight McGee Jr.

dwight.mcgee at gmail.com

"Problems cannot be solved at the same level of awareness that created them." 
                Albert Einstein

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