ADL: Magnezium charge and error message for flexible docking

manshu tang tangmanshu at yahoo.com
Tue Oct 16 06:49:17 PDT 2007


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? 
  
Thanks in advance!

Manshu Tang

       
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