[Dock-fans] Could Not Complete Growth Error

Trent E. Balius tbalius at aol.com
Tue Nov 27 10:43:21 PST 2012


 Hi,

You might also try runing dock with the verbose flag.  This might help isolate where dock is encountering problems.  

See the following:
http://mailman.docking.org/pipermail/dock-fans/2010-June/002392.html


Trent
 

-----Original Message-----
From: William Joseph Allen <william.joseph.allen at gmail.com>
To: Austin Baker <asb93 at pitt.edu>
Cc: dock-fans <dock-fans at docking.org>
Sent: Tue, Nov 27, 2012 10:37 am
Subject: Re: [Dock-fans] Could Not Complete Growth Error


Hi Austin,

How are you orienting the ligands? I assume you are using automated_matching = yes? If so, what is your sphere input file that you specify in the parameter file? If you open up the spheres in Chimera, do they fall where you expect with respect to your protein? If you also open up the box / grid, does it surround the spheres with a wide margin? Feel free to cut and paste the contents of your dock.in file so we can see whether there are any red flags.

Joe Allen





On Tue, Nov 27, 2012 at 1:23 PM, Austin Baker <asb93 at pitt.edu> wrote:

All,


	I am new to Dock and am having trouble running through the tutorials with my protein of interest. Thanks for the patience and help in advance.


	Every time that I try and dock a ligand I keep getting the same error message of:

 ERROR:  Could not complete growth.
         Confirm that the grid box is large enough to contain the ligand,
         and try increasing max_orientations.


I have tried searching through the archives and so far none of the options that are listed have helped. I have tried to increase the size of the box manually to a 30x30x30 box, increase the max conformers, played with the bump filter, the internal energy and use of the flexible ligand. In addition I have tried to dock something small like benzoic acid and cyclohexene but keep getting the same error messages.



Very much appreciated



Austin Baker
asb93 at pitt.edu
Graduate Student
Department of Chemistry
University of Pittsburgh


Everything is Experimental








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-- 
William Joseph Allen, Ph.D.
Robert C. Rizzo Research Group
Department of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/


 
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