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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