[Dock-fans] Fwd: query related to grid size

Trent E. Balius tbalius at aol.com
Sat Jan 28 09:31:38 PST 2012


I may not be clear on what you are trying to do.  But, . . .

If you are using multiple receptors you should first aline them.

Next you should select a common sets of spheres for generating a common box using showbox.  

You can force the two grids to have the same dimensions by using the same box.pdb for both receptors.  

Grid input file parameter: 

box_file [site_box.pdb] (float):
#PDB file containing showbox output which specifies boundaries of grid 


I hope this helps,
Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Trent E. Balius <tbalius at aol.com>
To: jir322 <jir322 at gmail.com>; dock-fans <dock-fans at docking.org>
Cc: minachitomar.bhubioinfo <minachitomar.bhubioinfo at gmail.com>
Sent: Sat, Jan 28, 2012 12:16 pm
Subject: Re: [Dock-fans] Fwd: query related to grid size



 Hi,

See the grid section of the manual:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Grid

See the docking tutorials located at the following link:

http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm
 
The first 3 tutorials will walk you through the process of preparing your receptor for docking.

Also, see the Rizzo lab tutorial:
http://ringo.ams.sunysb.edu/index.php/2011_DOCK_tutorial_with_Streptavidin

Note that you can visualize your grid with the program UCSF Chimera.

I hope that this helps,

 

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: John Irwin <jir322 at gmail.com>
To: dock-fans <dock-fans at docking.org>
Cc: minachitomar.bhubioinfo <minachitomar.bhubioinfo at gmail.com>
Sent: Fri, Jan 27, 2012 11:56 am
Subject: [Dock-fans] Fwd: query related to grid size


forwarded to the list. btw, it is free to upgrade to 6.5, which we
strongly advise.


---------- Forwarded message ----------
From: jyotisingh tomar <minachitomar.bhubioinfo at gmail.com>
Date: Fri, Jan 27, 2012 at 4:35 AM
Subject: query related to grid size
To: John Irwin <jir322 at gmail.com>



Dear Sir
               I an using  dock6.4 program and most of the time i m
facing problem while fixing grid size
in RNA range is ~ 25 for duplex DNA ~150 why it is so?
 in autodock we can visualize grid and fix easily is any easy way to
fix the grid size in dock also
--
hard work is key of success
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