[Dock-fans] RE: Atom valence violated error while running grid calculation

David.Maxwell at di.mdacc.tmc.edu David.Maxwell at di.mdacc.tmc.edu
Wed Aug 3 12:40:19 PDT 2005


Hi dock-fans,

I may have answered my own question.  Because of the distances to metal 
ion, there were bonds to the metal ion in the structure.  I forgot to 
delete those before writing out the .mol2 file.  Doing this seems to have 
eliminated to error I was seeing.  Sorry for any trouble.

-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
----- Forwarded by David Maxwell/RAD on 08/03/2005 02:35 PM -----


David Maxwell
08/03/2005 02:17 PM

 
        To:     dock-fans at docking.org
        cc: 
        Subject:        Atom valence violated error while running grid calculation

Hi dock-fans,

I am having some difficulty with a kinase structure that contains two Mg 
ions near to a an Asp group.  It is giving me the following error:

Reading in coordinates of receptor.
WARNING assign_vdw_labels: Atom valence violated for 1O6L **** ASP293 148 
OD2 1222.
Error reading in receptor.
Performing DOCK run

Without removing the Mg's entirely, what other suggestions would you have 
to address this error?

Thank you for your help

-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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