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PostPosted: Tue Dec 09, 2014 12:42 pm 
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Joined: Fri Nov 28, 2014 3:25 pm
Posts: 1
Hello there! I'm new to this forum and as well as for AutoDock.

I'm only starting to learn how to use this program so please bear with me. I've been learning to use AutoDock vina but as of lately I couldn't save pdbqt files in MGL Tools. I created the PDB files for the ligands from ChemDraw 3D. Would this be a compatible tool to create ligand files for Vina? However, my main concern is the inability to save PDBQT files. I've attached the error logs below. I hope someone can help me. Thanks! =)

Detect Root >>

Code:
>>> ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2389, in doit
    mol.LPO.autoroot()
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 929, in autoroot
    self.RBM.autoroot()
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 2139, in autoroot
    if not b.leaf:
AttributeError: Bond instance has no attribute 'leaf'


Save PDBQT >>

Code:
>>> ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1374, in doit
    mol.LPO.write(filename)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 888, in write
    self.writer.write(mol, outputfilename)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1073, in write
    ligand.torscount = len(ligand.allAtoms.bonds[0].get(lambda x:x.activeTors))
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\MolKit\tree.py", line 622, in get
    result = filter(selectionString, self.data)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1073, in <lambda>
    ligand.torscount = len(ligand.allAtoms.bonds[0].get(lambda x:x.activeTors))
AttributeError: Bond instance has no attribute 'activeTors'


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