[Dock-fans] some quetion of DOCK Anchor-and-Grow.

Trent E. Balius tbalius at aol.com
Wed Mar 27 07:37:10 PDT 2013


 

Hi,

In addition to visualizing the docking set-up to make sure all is well as Sudipto suggests, 
you might consider using the verbose flag (-v) to help identify where the sampling difficulties are.

   dock6 -v -i dock.in -o dock.out

 
See the following for more parameters that effect sampling:

   http://mailman.docking.org/pipermail/dock-fans/2013-March/002764.html

 
I hope this helps,


Trent
 

-----Original Message-----
From: Sudipto Mukherjee <sudmukh at yahoo.com>
To: 李雷 <284246396 at qq.com>; dock-fans <dock-fans at docking.org>
Sent: Wed, Mar 27, 2013 6:24 am
Subject: Re: [Dock-fans] some quetion of DOCK Anchor-and-Grow.



Hi 李雷,


The error you received indicates that no reasonable pose could be found during sampling. While DOCK suggests two possible reasons why this could happen, there might be other causes as well. 


Before attempting an actual virtual screen, it is a good idea to check your docking setup to make sure there are no obvious problems. First check the placement of the spheres used to orient the anchor. Are the spheres located within the target active site? Does the native ligand dock back in successfully? This error can occur when the ligand being docked in is simply too big to fit inside the active site. How many rotatable bonds are present in the ligand you are attempting to dock in. DOCK is designed primarily with screening small molecules in mind. 

 
Regards
Sudipto Mukherjee, PhD
Dept. of Chemistry, Temple University

1901 N 13th St, Philadelphia, PA 19122



  
 
 
  
  From: 李雷 <284246396 at qq.com>
 To: dock-fans <dock-fans at docking.org> 
 Sent: Wednesday, March 27, 2013 4:42 AM
 Subject: [Dock-fans] some quetion of DOCK Anchor-and-Grow.
  
 

Hi everyone,
     I have used DOCK6.5 to do some work about virtual screen. when I execute DOCK of a target protein and a random ligand use Anchor-and-Grow method, there are some information feedback as follows:

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


so I try to increase the size of BOX,from 6.0A to 8.0 10.0 12.0 but it still  report errors;I also increase the default max_orientations 500 to 1500 2000 even 10000 but the error was still exist.
could anyone  tell me the reason and how to deal with this question. Thankyou very much !
Regard,


LL_thuder


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