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专业: 理论和计算化学

[求助] 新手关于autodock准备ligand分子时出现的问题已有1人参与

我是在window xp系统上装的ADT，在准备ligand配体分子时，open分子时弹出一下页面：  （请教是什么问题，怎么解决？）

Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32
Type "copyright", "credits" or "license()" for more information.

****************************************************************
Personal firewall software may warn about the connection IDLE
makes to its subprocess using this computer's internal loopback
interface.  This connection is not visible on any external
interface and no data is sent to or received from the Internet.
****************************************************************

IDLE 1.2.2    ==== No Subprocess ====
>>> 02: :CYS1:HT2 and 02: :CYS1:HT3 have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Python25\Lib\site-packages\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues=False)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
  File "C:\Python25\Lib\site-packages\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
  File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
  File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
  File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [-11.763, 0.56000000000000005, -0.13400000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001])
02: :CYS1:HT2 and 02: :CYS1:HT3 have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Python25\Lib\site-packages\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues=False)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
  File "C:\Python25\Lib\site-packages\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
  File "C:\Python25\Lib\site-packages\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
  File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
  File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
  File "C:\Python25\Lib\site-packages\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [-11.763, 0.56000000000000005, -0.13400000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001], [-11.365, 1.5389999999999999, -0.16600000000000001])

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