[Dock-fans] Scoring without docking

David.Maxwell at di.mdacc.tmc.edu David.Maxwell at di.mdacc.tmc.edu
Tue Aug 9 11:24:37 PDT 2005


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
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