I got a problem while using Autodocktools, when it comes to Run-->Autogrid or Autodock, there is always an error as the attached figure shows. I tried both window and linux versions, both of them give this error, it seems that the program could not find the specified .py file, but when I check these directory, the .py files were there, why the program say no such file or directory could be found? Thanks! Cheers!
First of all, the application CAN find the python files(VF.py and subprocess.py), the error states that some file is missing from an attempt on line 1097 of subprocessing module, which function is to load binaries into python, specifically: "autodock3 –p file.dpf –l file.dlg &" or "autogrid3 –p file.gpf –l file.glg &"
probably, the autodock2 / autogrid3 aren't installed or they aren't on your PATH. Even the dpf/dlg/gpf/glg file could be missing.
Try to run on terminal autodock2 or autogrid3, if it works, look for dpf/dlg/gpf/glg file.
Thanks Paolo! You are right! I copied the autodock and autogrid program files into the autodocktool folder and it works. It seems that autodock and autogrid program must be installed in the same folder as the mgl tool suite! May be addition of the autodock and autogrid directory to the PATH could also solve the problem. But copy the file sounds more straight forward!
Hello,
I have a similar issue but in the ligand preparation part. I get an error box like you and when I try to settle the torsion tree parameters, the software replies that the ligand is not selected, although I had previously selected it in the left section of the dashboard. What do you suggest in this case?
Thanks!
Hi Ana, could you post details of the error you have? Paolo may a better idea what is going on. One thing you could check is to make sure that you have administer right on your computer. Because the autodock tool doesn't call any external command until it gets to autogrid and autodock, so everything should be fine as long as you have the administer right to your computer.
the error box I get is like 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 ====
>>> forcing addition of gasteiger charges to molecule with all zero charges
GACZIT (Escin Ia):default:RES2:O25 and GACZIT (Escin Ia):default:RES2:O25 have the same coordinates
ERROR ****************************** ***************
Traceback (most recent call last):
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\ViewerFramework\VF. py", line 898, in tryto
result = command( *args, **kw )
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files\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\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues= False)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges( mol.allAtoms)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\MolKit\ chargeCalculator.py", line 80, in addCharges
babel.assignHybridization( atoms)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\PyBabel\atomTypes.py" , line 137, in assignHybridization
self.valence_two()
File "C:\Program Files\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\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:', [2.3683000000000001, 5.9660000000000002, 14.5594], [2.3683000000000001, 5.9660000000000002, 14.5594], [2.3683000000000001, 5.9660000000000002, 14.5594])
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Program Files\MGLTools-1.5.6\lib\lib- tk\Tkinter.py", line 1403, in __call__
return self.func(*args)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ autotorsCommands.py", line 810, in chooseLigand_cb
mols = self.chooser.getMolSet()
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\Pmv\guiTools.py", line 178, in getMolSet
if self.mode=='single': return mols[0]
File "C:\Program Files\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
forcing addition of gasteiger charges to molecule with all zero charges
GACZIT (Escin Ia)_2:default:RES2:O25 and GACZIT (Escin Ia)_2:default:RES2:O25 have the same coordinates
ERROR ****************************** ***************
Traceback (most recent call last):
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\ViewerFramework\VF. py", line 898, in tryto
result = command( *args, **kw )
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ autotorsCommands.py", line 1008, in doit
initLPO4(mol, cleanup=cleanup)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ autotorsCommands.py", line 292, in initLPO4
root=root, outputfilename=outputfilename, cleanup=cleanup)
File "C:\Program Files\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\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ MoleculePreparation.py", line 768, in __init__
delete_single_nonstd_residues= False)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\AutoDockTools\ MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges( mol.allAtoms)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\MolKit\ chargeCalculator.py", line 80, in addCharges
babel.assignHybridization( atoms)
File "C:\Program Files\MGLTools-1.5.6\lib\site- packages\PyBabel\atomTypes.py" , line 137, in assignHybridization
self.valence_two()
File "C:\Program Files\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\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:', [2.3683000000000001, 5.9660000000000002, 14.5594], [2.3683000000000001, 5.9660000000000002, 14.5594], [2.3683000000000001, 5.9660000000000002, 14.5594])
Hey Ana,
The first line of the error message( GACZIT (Escin Ia):default:RES2:O25 and GACZIT (Escin Ia):default:RES2:O25 have the same coordinates ) states that two Escin Ia oxigens are potentially duplicated(and it causes the "division by zero" error), but if you're sure that there are no duplicates, possibly spurious bonds are created when the molecule is loaded to be converted as PDBQT.
Try to minimize it and see if the problem persists.
Yes, I think it is a structural error(duplication) or a parsing issue. On both case, you can try minimize your sequence with Amber or Babel and try again. If it fails, would be easier to help if you provide the structure.
Well Ana, the start is always the hardest step. But we eventually learn, so take your time.
About the packages that you still don't know:
Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids. You can find it files and tutorials at http://ambermd.org
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. You can find it at: http://openbabel.org/
I hope you can use one of them to solve your structural problem. If not, just ask for more help.
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