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 Post subject: Ligand file
PostPosted: Wed May 14, 2014 6:13 pm 
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Joined: Wed May 14, 2014 5:57 pm
Posts: 2
Hello -

I am beginner user of AutoDock and I have installed the Windows version of MGL 1.5.6 ( I believe that the install was successful).

I am running ADT to set up the ligand and receptor. My receptor has a zinc atom and my ligand is something I have built by drawing the structure (nothing fancy - your standard aromatic heterocyclic molecule with an aliphatic sidechain).

I had read in the ligand and there were no errors when setting the Gasteiger forcefields. Then I set up the number of torsions to 6 within the Torsion tree section of the ligand module (I received no errors at this stage). So I proceeded to write the randomized structure to a pdbqt file; I got a Python script error message (included below). Please can you help this novice user of ADT interpret this error and please can you propose a solution?

Also I am wondering if the aromatic rings are not represented by their kekule representation?

Sincerely
Jayashree Srinivasan
(619)-847-4145


IDLE 1.2.2 ==== No Subprocess ====
>>> ERROR *********************************************
Traceback (most recent call last):
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\AutoDockTools\autotorsCommands.py", line 1505, in doit
LR = LigandRandomizer(mol, outputfilename, info_lo=info_lo, info_hi=info_hi, ntries=ntries, torsOnly=torsOnly, relTrans=relTrans, verbose=verbose)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1499, in __init__
assert hasattr(m, 'torTree'), "specified ligand does not have a torsion tree"
AssertionError: specified ligand does not have a torsion tree
ERROR *********************************************
Traceback (most recent call last):
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\AutoDockTools\autotorsCommands.py", line 1505, in doit
LR = LigandRandomizer(mol, outputfilename, info_lo=info_lo, info_hi=info_hi, ntries=ntries, torsOnly=torsOnly, relTrans=relTrans, verbose=verbose)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1705, in __init__
v1 = b.possibleTors
AttributeError: Bond instance has no attribute 'possibleTors'
ERROR *********************************************
Traceback (most recent call last):
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\AutoDockTools\autotorsCommands.py", line 1885, in doit
self.getNeighbors(mol.ROOT)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1902, in getNeighbors
notActBonds = filter(lambda x: x.activeTors!=1, at.bonds)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1902, in <lambda>
notActBonds = filter(lambda x: x.activeTors!=1, at.bonds)
AttributeError: Bond instance has no attribute 'activeTors'
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 1403, in __call__
return self.func(*args)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2102, in guiCallback
self.vf.ADtors_defineRotBonds.buildCol()
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2452, in buildCol
torscount = len(mol.allAtoms.bonds[0].get(lambda x: x.activeTors))
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\tree.py", line 622, in get
result = filter(selectionString, self.data)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2452, in <lambda>
torscount = len(mol.allAtoms.bonds[0].get(lambda x: x.activeTors))
AttributeError: Bond instance has no attribute 'activeTors'
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 1403, in __call__
return self.func(*args)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2763, in guiCallback
self.setUpDisplay()
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2758, in setUpDisplay
self.displayForm()
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2845, in displayForm
torscount = len(mol.allAtoms.bonds[0].get(lambda x: x.activeTors))
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\tree.py", line 622, in get
result = filter(selectionString, self.data)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2845, in <lambda>
torscount = len(mol.allAtoms.bonds[0].get(lambda x: x.activeTors))
AttributeError: Bond instance has no attribute 'activeTors'
WARNING: Spatial Logic module not found
ERROR *********************************************
Traceback (most recent call last):
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\AutoDockTools\autotorsCommands.py", line 1505, in doit
LR = LigandRandomizer(mol, outputfilename, info_lo=info_lo, info_hi=info_hi, ntries=ntries, torsOnly=torsOnly, relTrans=relTrans, verbose=verbose)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1705, in __init__
v1 = b.possibleTors
AttributeError: Bond instance has no attribute 'possibleTors'
ERROR *********************************************
Traceback (most recent call last):
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\AutoDockTools\autotorsCommands.py", line 1505, in doit
LR = LigandRandomizer(mol, outputfilename, info_lo=info_lo, info_hi=info_hi, ntries=ntries, torsOnly=torsOnly, relTrans=relTrans, verbose=verbose)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1504, in __init__
ndihe = len(m.allAtoms.bonds[0].get(lambda x: x.activeTors==True))
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\tree.py", line 622, in get
result = filter(selectionString, self.data)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1504, in <lambda>
ndihe = len(m.allAtoms.bonds[0].get(lambda x: x.activeTors==True))
AttributeError: Bond instance has no attribute 'activeTors'


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