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新手关于autodock准备ligand分子时出现的问题 已有1人参与
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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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