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PostPosted: Tue May 10, 2016 12:19 pm 
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Joined: Tue May 10, 2016 12:00 pm
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Hello everyone ,

After the docking of a protein with its ligand, I got with vina possible orientations of the ligand in the binding site.
I will now try to bind a further ligand in an allosteric site of the protein.

The problem is that, preparing the ligand with AutoDock, I get the error:

File "C: \ Program Files (x86) \ MGLTools-1.5.6 \ lib \ site-packages \ ViewerFramework \ VF.py", line 898, in tryto
result = command (* args, ** kw)
File "C: \ Program Files (x86) \ MGLTools-1.5.6 \ lib \ site-packages \ VMS \ editCommands.py", line 1027, in doit
babel.assignHybridization (mol.allAtoms)
File "C: \ Program Files (x86) \ MGLTools-1.5.6 \ lib \ site-packages \ PyBabel \ atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number (a.babel_type)
File "C: \ Program Files (x86) \ MGLTools-1.5.6 \ lib \ site-packages \ PyBabel \ atomTypes.py", line 103, in get_atomic_number
(Name, _name))
ValueError: Could not find atomic number for A A

What should I do ?


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