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PostPosted: Tue Mar 15, 2016 7:24 am 
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Joined: Mon Mar 14, 2016 8:45 am
Posts: 3
Hi all,

Recently we faced a tough probelm about docking experiment of nitrile hydratase. We can run AutoDock successfully, but when it comes to the final analysis, there is always a mistake. The receptor contains a cobalt ion as well as two non-standard Cys residues in its active site. Is there something wrong with our AD4_parameters.dat file?

Any suggestions would be greatly appreciated. Thanks!


*Python Shell*
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/ViewerFramework/VF.py", line 929, in tryto
result = command( *args, **kw )
File "/usr/lib/python2.7/dist-packages/AutoDockTools/autoanalyzeCommands.py", line 3087, in doit
self.build()
File "/usr/lib/python2.7/dist-packages/AutoDockTools/autoanalyzeCommands.py", line 2922, in build
self.buildLigandDisplay()
File "/usr/lib/python2.7/dist-packages/AutoDockTools/autoanalyzeCommands.py", line 2788, in buildLigandDisplay
self.vf.computeMSMS(lig, surfName, perMol=1, topCommand=0, display=self.showMsms.get())
AttributeError: MoleculeViewer instance has no attribute 'computeMSMS'
Unable to assign HYB type to atom Co
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/ViewerFramework/VF.py", line 929, in tryto
result = command( *args, **kw )
File "/usr/lib/python2.7/dist-packages/AutoDockTools/autoanalyzeCommands.py", line 3087, in doit
self.build()
File "/usr/lib/python2.7/dist-packages/AutoDockTools/autoanalyzeCommands.py", line 2922, in build
self.buildLigandDisplay()
File "/usr/lib/python2.7/dist-packages/AutoDockTools/autoanalyzeCommands.py", line 2788, in buildLigandDisplay
self.vf.computeMSMS(lig, surfName, perMol=1, topCommand=0, display=self.showMsms.get())
AttributeError: MoleculeViewer instance has no attribute 'computeMSMS'


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File comment: original files used in my autodock
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