ADL: Magnezium charge and error message for flexible docking

Yang Ye leafyoung at yahoo.com
Tue Oct 16 09:21:03 PDT 2007


On 10/16/2007 9:49 PM, manshu tang wrote:
> Hi fellow autodockers
>      I'm new in this field and is trying to dock some
> small compounds to a protein. 
>      One question I'm facing all the time is that
> autodock tools always says the magnezium within the
> protein is not charged.When I tried to preparing the
> flexible residue file a python shell display some
> error message. first is "unable to assign valence to
> Mg, Unable to assign HAD type to Mg, " followed by
> "Sorry, there are no Gasteiger parameters available
> for Mg. Unable to assign MAP type to atom Mg" then is
> several line of red words:   
> File
> "/Library/MGLTools/1.4.6/MGLToolsPckgs/ViewerFramework/VF.py",
> line 714, in tryto
>     result = apply( command, args, kw )
>   File
> "/Library/MGLTools/1.4.6/MGLToolsPckgs/AutoDockTools/autoflexCommands.py",
> line 371, in doit
>     map(self.setAutoFlexFields, flex_residues)
>   File
> "/Library/MGLTools/1.4.6/MGLToolsPckgs/AutoDockTools/autoflexCommands.py",
> line 413, in setAutoFlexFields
>     rotatables = rbs.select(bondlist).....
>
>
> Could someone tell how to add charge to the magnezium
> and what's the meaning of the red line message and how
> to deal with it? 
>   
You can safely leave the line of Mg inside your pdbqt, assign a charge 
to it (+0.8 ~ +1.2e).

script prepare_dpf4.py and prepare_gpf4.py know to deal with it. So do 
autogrid4 and autodock4.
>   
> Thanks in advance!
>
> Manshu Tang
>
>        
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