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PostPosted: Thu May 21, 2015 3:56 pm 
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Joined: Thu May 21, 2015 3:48 pm
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I am using AutoDock Tools to on Windows 7 (64 bit) to create a .pdbqt from a .pdb file. On selecting Grid->Macromolecule ->Choose->Select Molecule I got the following error output. I have attached the .pdb file below. Many thanks.

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 (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\Pmv\editCommands.py", line 1043, in doit
hat = addh.addHydrogens(mol.allAtoms, method=method)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\addh.py", line 92, in addHydrogens
Hatoms = self.place_hydrogens1(atoms, num_H_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\addh.py", line 156, in place_hydrogens1
Hat = Hat + self.add_vinyl_hydrogens(a ,SP2_C_H_DIST)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\addh.py", line 444, in add_vinyl_hydrogens
c3 = c2.bonds[1].atom1
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\UserList.py", line 28, in __getitem__
def __getitem__(self, i): return self.data[i]
IndexError: list index out of range
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\autogpfCommands.py", line 3904, in doit
ad4_typer.setAutoDockElements(mol)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\atomTypeTools.py", line 370, in setAutoDockElements
ah.assignHybridization(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 103, in get_atomic_number
(name,_name) )
ValueError: Could not find atomic number for 1 1
adding gasteiger charges to pSRII_88
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\Pmv\editCommands.py", line 2593, in doit
babel.assignHybridization(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 103, in get_atomic_number
(name,_name) )
ValueError: Could not find atomic number for 1 1
charges on carbons unchanged
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\Pmv\editCommands.py", line 3579, in doit
chs = Numeric.sum(item.atoms.charge)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\molecule.py", line 136, in __getattr__
res.append(a._charges[a.chargeSet])
KeyError: None
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\autogpfCommands.py", line 4334, in doit
errCharge, resList = checkMolCharges(mol, self.vf)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 204, in checkMolCharges
totalCharge,resList = vf.checkResCharges(mol, topCommand=0)
ValueError: too many values to unpack
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\autogpfCommands.py", line 3904, in doit
ad4_typer.setAutoDockElements(mol)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\atomTypeTools.py", line 370, in setAutoDockElements
ah.assignHybridization(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 103, in get_atomic_number
(name,_name) )
ValueError: Could not find atomic number for 1 1
adding gasteiger charges to pSRII_88
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\Pmv\editCommands.py", line 2593, in doit
babel.assignHybridization(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 103, in get_atomic_number
(name,_name) )
ValueError: Could not find atomic number for 1 1
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\Pmv\editCommands.py", line 3579, in doit
chs = Numeric.sum(item.atoms.charge)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\molecule.py", line 136, in __getattr__
res.append(a._charges[a.chargeSet])
KeyError: None
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\autogpfCommands.py", line 4334, in doit
errCharge, resList = checkMolCharges(mol, self.vf)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 204, in checkMolCharges
totalCharge,resList = vf.checkResCharges(mol, topCommand=0)
ValueError: too many values to unpack


Attachments:
pSRII_88.zip [62.56 KiB]
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