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.

hello Paolo,

thaks for your tip! I really don't understand how this happens when I open the structure, do you think it can be a structural error? I haven't changed the structure, I just downloaded it from the database and then used it in the software. 

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.

Ok, I'm really new to the program (1st time using it), so I don't even know Amber or Babel that you mentioned :) I tried to follow a tutorial on autodock so that I can learn how to use it nad I got stuck on the ligand preparation....

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.