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[AutoDock&Vina] 在打开autodock小分子配体的时候出现的问题,向各位前辈请教

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发表于 2019-11-9 20:32:17 | 显示全部楼层 |阅读模式

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forcing addition of gasteiger charges to molecule with all zero charges
[14C](=O)=O:default:<0>:C1 and [14C](=O)=O:default:<0>:O2 have the same coordinates
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 1008, in doit
    initLPO4(mol, cleanup=cleanup)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
    root=root, outputfilename=outputfilename, cleanup=cleanup)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__
    detect_bonds_between_cycles=detect_bonds_between_cycles)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
    delete_single_nonstd_residues=False)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
    self.addCharges(mol, charges_to_add)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
    chargeCalculator.addCharges(mol.allAtoms)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
    babel.assignHybridization(atoms)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
    self.valence_two()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
    angle1 = bond_angle(k.coords, a.coords, l.coords)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
    raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0])
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