[Dock-fans] Scoring without docking

Terry Lang terry at cgl.ucsf.edu
Wed Aug 10 15:49:42 PDT 2005


Dear David,

          First, yes, this is the correct way to rescore a pose without 
moving the ligand.  For the energies, the differences you are getting 
are within the precision limits of the two types of calculations you are 
running.  For the docking calculation, all the numbers have been read in 
and modified during the calculation.  As a result, they are stored at 
the full precision allowed by the compiler/operating system.  In the 
rescoring calculation, the program is reading in information from a 
number of different files with varying levels of precision.  As a 
result, you will see differences in the thousandth and smaller decimal 
places that reflect this issue.  This effect is therefore a result of 
the limitations of I/O and is well within the error of the calculation.

Sincerely,
Terry

David.Maxwell at di.mdacc.tmc.edu wrote:

>Hi Dock-fans,
>
>As a follow-up to my own message, I did the following to attempt just the 
>scoring on 12 ligands previously docked and scored:
>
>orient_ligand no
>flexible_ligand no
>minimize_ligand no
>minimize_anchor no
>minimize_flexible_growth no
>minimize_final_pose no
>
>Is this the correct method to score "as-is" or is there an easier way? The 
>results I get back are not exactly the same, but different by around 0.001 
>in terms of score.  Not knowing the internals of the code, is this within 
>error limits?
>
>-Dave
>_____________________________________________
>David Maxwell, Ph.D.
>Senior Research Scientist
>Dept. of Experimental Diagnostic Imaging
>University of Texas M.D. Anderson Cancer Center
>8012 El Rio St.
>Houston, TX 77054
>Phone: (713)-563-9963     Fax: (713)-563-0084
>david.maxwell at di.mdacc.tmc.edu
>
>
>
>
>David.Maxwell at di.mdacc.tmc.edu
>Sent by: dock-fans-bounces at docking.org
>08/09/2005 12:35 PM
>
> 
>        To:     dock-fans at docking.org
>        cc: 
>        Subject:        [Dock-fans] Scoring without docking
>
>
>Hi Dock-fans,
>
>I know this is not the proper use of Dock, but what are the combination of 
>
>flags to get Dock 5.2 to just score the compounds with the coordinates 
>listed in the .mol2 file.  I have tried turning off the "orient_ligand" 
>flag, but it doesn't seem to calculate anything.
>
>-Dave
>
>_____________________________________________
>David Maxwell, Ph.D.
>Senior Research Scientist
>Dept. of Experimental Diagnostic Imaging
>University of Texas M.D. Anderson Cancer Center
>8012 El Rio St.
>Houston, TX 77054
>Phone: (713)-563-9963     Fax: (713)-563-0084
>david.maxwell at di.mdacc.tmc.edu
>_______________________________________________
>Dock-fans mailing list
>Dock-fans at docking.org
>http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
>
>
>_______________________________________________
>Dock-fans mailing list
>Dock-fans at docking.org
>http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>  
>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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