I want to try docking a metal ion like Cd(II) to an enzyme. But I cannot open my Cd.pdbqt file in AutoDock tools as the ligand. It pops up an error file.
I downloaded the coordinates of the metal ion in sdf format and using OpenBabel I converted the .sdf to .pdbqt format. But when I open the pdbqt file in AutoDock Tools with Ligand==>Input==>Open and select the pdbqt file an error occurs. The error is given bellow.
Python 2.7.11 (v2.7.11:6d1b6a68f775, Dec 5 2015, 20:32:19) [MSC v.1500 32 bit (Intel)] on win32
Type "copyright", "credits" or "license()" for more information.
==== No Subprocess ====
>>> {'gui': None, 'cmd': <Pmv.selectionCommands.MVSelectCommand instance at 0x0F152BE8>, 'name': 'select'}
{'gui': None, 'cmd': <Pmv.selectionCommands.MVDeSelectCommand instance at 0x0F156210>, 'name': 'deselect'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152F58>, 'cmd': <Pmv.selectionCommands.MVClearSelection instance at 0x0F156468>, 'name': 'clearSelection'}
{'gui': None, 'cmd': <Pmv.selectionCommands.MVExpandSelection instance at 0x0F156530>, 'name': 'expandSelection'}
{'gui': None, 'cmd': <Pmv.selectionCommands.MVSelectAround instance at 0x0F156580>, 'name': 'selectAround'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152FA8>, 'cmd': <Pmv.selectionCommands.MVSaveSetCommand instance at 0x0F156EE0>, 'name': 'saveSet'}
{'gui': None, 'cmd': <Pmv.selectionCommands.MVCreateSetIfNeeded instance at 0x0F156968>, 'name': 'createSetIfNeeded'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152B98>, 'cmd': <Pmv.selectionCommands.MVInvertSelection instance at 0x0F156A08>, 'name': 'invertSelection'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152508>, 'cmd': <Pmv.selectionCommands.MVSelectSetCommand instance at 0x0F156F80>, 'name': 'selectSet'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152B70>, 'cmd': <Pmv.selectionCommands.MVSelectFromStringCommand instance at 0x0F156DC8>, 'name': 'selectFromString'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152B48>, 'cmd': <Pmv.selectionCommands.MVDirectSelectCommand instance at 0x0F156760>, 'name': 'directSelect'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152BC0>, 'cmd': <Pmv.selectionCommands.MVSelectSphericalRegion instance at 0x0F161698>, 'name': 'selectInSphere'}
{'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0x0F152C10>, 'cmd': <Pmv.selectionCommands.SelectNoWaterHeteroAtomsCommand instance at 0x0F161198>, 'name': 'selectHeteroAtoms'}
forcing addition of gasteiger charges to molecule with all zero charges
cd: :UNL1:CD and cd: :UNL1:CD have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 941, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1010, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1016, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 765, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 141, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 227, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [2.0, 0.0, 0.0], [2.0, 0.0, 0.0], [2.0, 0.0, 0.0])
[DEBUG ON]
>>>
[DEBUG OFF]
>>> forcing addition of gasteiger charges to molecule with all zero charges
cd: :UNL1:CD and cd: :UNL1:CD have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 941, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1010, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1016, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 765, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 141, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 227, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [2.0, 0.0, 0.0], [2.0, 0.0, 0.0], [2.0, 0.0, 0.0])
forcing addition of gasteiger charges to molecule with all zero charges
cd: :UNL1:CD1 and cd: :UNL1:CD1 have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 941, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1010, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1016, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 765, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 141, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 227, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [2.0, 0.0, 0.0], [2.0, 0.0, 0.0], [2.0, 0.0, 0.0])
forcing addition of gasteiger charges to molecule with all zero charges
Unable to assign MAP type to atom As
Sorry, there are no Gasteiger parameters available for atom as: :UNL1:AS
Unable to assign XYZ type to atom As
Unable to assign HYB type to atom As
Unable to assign HYB type to atom As
Unable to assign XYZ type to atom As
Unable to assign HYB type to atom As
Unable to assign HYB type to atom As
Unable to assign XYZ type to atom As
Unable to assign HYB type to atom As
Unable to assign HYB type to atom As
forcing addition of gasteiger charges to molecule with all zero charges
cd: :UNL1:CD and cd: :UNL1:CD have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 941, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1010, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1016, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 765, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 141, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 227, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0])
forcing addition of gasteiger charges to molecule with all zero charges
cd: :UNL1:CD and cd: :UNL1:CD have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 941, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1010, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1016, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 765, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 141, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 227, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0])
My cd.sdf file used to convert to cd.pdbqt format is;
CD
-OEChem-08112316133D
1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 Cd 0 2 0 0 0 0 0 0 0 0 0 0
M CHG 1 1 2
M END
> <OPENEYE_ISO_SMILES>
[Cd+2]
> <OPENEYE_INCHI>
InChI=1S/Cd/q+2
> <OPENEYE_INCHIKEY>
WLZRMCYVCSSEQC-UHFFFAOYSA-N
> <FORMULA>
Cd+2
$$$$
And converted cd.pdbqt file:
REMARK Name = CD
REMARK 0 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 CD UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 Cd
ENDROOT
TORSDOF 0
Please help me in solving this. What is the mistake here for the error? Or can't I do the docking of a metal ion to an enzyme?