[Dock-fans] inquiry on Dock 6.2

Trent Balius tbalius at aol.com
Tue Nov 17 17:01:34 PST 2009


 Hi Ethel,


The parameter you should change is the following:



num_scored_conformers   10

Dock generates the same answers (for the same binary, on the same platform, and the same input file); so, rerunning dock will not help.

Note the cluster heads are diverse poses. You may wish to turn clustering off. 

see the manual for
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput

 
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
 

 

-----Original Message-----
From: ethel urzo <reau_05 at yahoo.com>
To: dock-fans at docking.org
Sent: Tue, Nov 17, 2009 6:31 pm
Subject: [Dock-fans] inquiry on Dock 6.2













Hi!

May I know how can I run DOCK 6.2 so that it would give 10 results (interaction
energies)?
is there any parameter in the DOCK synonymous to "number of runs/trials" which is adjustable?
Or I have to repeat the whole process 10 times just to obtain 10 results?
I am working with my undergraduate thesis and my adviser requires me 10 data for each ligand and then I'll get the mean..

Thank You.

Ethel Urzo








      
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