Question: What does my error message (Autodock vina ligand error) mean ?
0
gravatar for akansha.gitanjali
4 weeks ago by
akansha.gitanjali0 wrote:

I have a problem with autodock vina.

I made a ligand on pubchem and converted it to pdb. When I tried uploading it to Autodock tools it is giving a error (pasted the error message below). Can you detect what is the problem all about?

It will be very helpful if anyone can help me with this.

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 ====
>>> SI_4: :UNK0:H and SI_4: :UNK0:H have the same coordinates
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\autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\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 (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\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 (x86)\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:', [334.529, 216.50800000000001, 0.0], [334.529, 216.50800000000001, 0.0], [334.529, 216.50800000000001, 0.0])
SI_1: :UNK2:H and SI_1: :UNK2:H have the same coordinates
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\autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files (x86)\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 (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues=False)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\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 (x86)\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:', [322.80900000000003, 157.24299999999999, 0.0], [322.80900000000003, 157.24299999999999, 0.0], [322.80900000000003, 157.24299999999999, 0.0])
software error • 122 views
ADD COMMENTlink modified 4 weeks ago by pq0ky0 • written 4 weeks ago by akansha.gitanjali0
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gravatar for pq0ky
4 weeks ago by
pq0ky0
pq0ky0 wrote:

You can Try From here Emergency IT Support

ADD COMMENTlink written 4 weeks ago by pq0ky0
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