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

Xiao Zhu zhu at outerbanks.umaryland.edu
Wed Aug 3 12:49:16 PDT 2005


In the mol2 file, make sure there is no bond between the Mg ions and
the Asp. There's probably a covalent bond that is not supposed to be
there. Check the structure and let me know.

On Wed, 3 Aug 2005 David.Maxwell at di.mdacc.tmc.edu wrote:

> 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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