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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » DS/Sybyl/Autodock » autodock tool导入macromolecule后再导入ligand就出错了
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ming142007

铁杆木虫 (职业作家)

化学百科

[求助] autodock tool导入macromolecule后再导入ligand就出错了

autodock tool导入macromolecule后再导入ligand就出错了，弹出内容如下，求助，不知道是什么原因：



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 ====
>>> 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\autostartCommands.py", line 964, in doit
    ps = subprocess.Popen(args)
  File "C:\Program Files\MGLTools-1.5.6\lib\subprocess.py", line 594, in __init__
    errread, errwrite)
  File "C:\Program Files\MGLTools-1.5.6\lib\subprocess.py", line 816, in _execute_child
    startupinfo)
WindowsError: [Error 2]
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\autostartCommands.py", line 964, in doit
    ps = subprocess.Popen(args)
  File "C:\Program Files\MGLTools-1.5.6\lib\subprocess.py", line 594, in __init__
    errread, errwrite)
  File "C:\Program Files\MGLTools-1.5.6\lib\subprocess.py", line 816, in _execute_child
    startupinfo)
WindowsError: [Error 2]
adding gasteiger charges to  ADTPDBHSA
1H9Z:A:HOH2001:O and 1H9Z:A:HOH2001:O have the same coordinates
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 1008, in doit
    initLPO4(mol, cleanup=cleanup)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
    root=root, outputfilename=outputfilename, cleanup=cleanup)
  File "C:\Program Files\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\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
    delete_single_nonstd_residues=False)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
    self.addCharges(mol, charges_to_add)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
    chargeCalculator.addCharges(mol.allAtoms)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
    babel.assignHybridization(atoms)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
    self.valence_two()
  File "C:\Program Files\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\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:', [52.0, 20.254999999999999, 31.460999999999999], [52.0, 20.254999999999999, 31.460999999999999], [52.0, 20.254999999999999, 31.460999999999999])
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1楼 2013-04-05 22:01:59
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longytu

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★
ben_ladeng: 金币+1, 谢谢交流 2013-04-05 22:29:26
1：是不是在grid一步出现的问题呢？重启软件试试
2：你的大小分子是否在同一个路径中，确保此路径没有中文
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2楼2013-04-05 22:23:45
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