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

Trent E. Balius tbalius at aol.com
Mon Jan 30 06:32:58 PST 2012





 Hi Jyoti,

The grid dimensions are determined by the box.pdb.  

the box.pdb file is generated by the showbox program:

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

The following is an excerpt from a docking tutorial
http://ringo.ams.sunysb.edu/index.php/2011_DOCK_tutorial_with_Streptavidin

########
Create a showbox.in file as follows:

Y
5.0                            
selected_spheres.sph   
1                       
1DF8.box.pdb

Type 'showbox < showbox.in'
########

The box margin is 5 angstroms,  this is the space add to the spheres.  If you increase this number the box will get larger.

I would recommend that you visualize your spheres and make sure that the spheres overlap with the ligand.

Then I recommend that you generate and visualize the box.pdb and verify that your ligand is contained in the box.

Then generate your grid and perform docking.    

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: jyotisingh tomar <minachitomar.bhubioinfo at gmail.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Mon, Jan 30, 2012 12:30 am
Subject: Re: [Dock-fans] Fwd: query related to grid size


many thanks for answering, but my problem is still unsolved
I am working on G-quadruplex DNA my problem is that my ligand is not coming inside the grid box, after dock run i m opening grid, receptor and docked ligand in pymol but docked ligand is outside of box so to fix size of grid box so that ligand get inside?  


On Sat, Jan 28, 2012 at 11:01 PM, Trent E. Balius <tbalius at aol.com> wrote:

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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-- 
hard work is key of success

 
 
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