mzbylzs 发表于 2016-12-28 14:42:04

请问ligand处理时无法检测root,choose torsions报错

大家好
      我用ZINC上下载的mol2格式,用chem3D转的pdb格式的tetradotoxin作为配体,
Autodock在处理TTX时,检测root与choose torsions会报错,内容为
Traceback (most recent call last):
File "F:\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
File "F:\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 2389, in doit
    mol.LPO.autoroot()
File "F:\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 929, in autoroot
    self.RBM.autoroot()
File "F:\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'




Traceback (most recent call last):
File "F:\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
File "F:\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1374, in doit
    mol.LPO.write(filename)
File "F:\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 888, in write
    self.writer.write(mol, outputfilename)
File "F:\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1073, in write
    ligand.torscount = len(ligand.allAtoms.bonds.get(lambda x:x.activeTors))
File "F:\MGLTools-1.5.6\lib\site-packages\MolKit\tree.py", line 622, in get
    result = filter(selectionString, self.data)
File "F:\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1073, in <lambda>
    ligand.torscount = len(ligand.allAtoms.bonds.get(lambda x:x.activeTors))
AttributeError: Bond instance has no attribute 'activeTors'

请问可能是分子结构的问题嘛?用示例的hsg1与Ind可以顺利做到对接完,但换成自己要做的pdb就有很多问题
系统为win7 32位,谢谢!!

mzbylzs 发表于 2016-12-29 09:03:53

请问计算到最后,analysis-dockings-show interactions,报错为
ValueError: dimensions too large.
该怎么修改才能继续呢

mzbylzs 发表于 2017-1-3 18:58:29

后续用pymol做了

白杨 发表于 2017-1-25 12:25:23

autodock 打开ligand时可以选择mol2格式打开,试一下这样会不会报错?
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