[Dock-fans] Could Not Complete Growth Error

William Joseph Allen william.joseph.allen at gmail.com
Tue Nov 27 10:37:24 PST 2012


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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