ADL: Error loading AutoDock Tools

venkat vkabas at yahoo.com
Mon Jun 22 15:21:10 PDT 2009


Hi 
I am trying to run prepare_ligand, I got following error message in between


00284.nci_2.mol2
setting PYTHONHOME environment
Traceback (most recent call last):
  File "prepare_ligand4.py", line 153, in <module>
    mols = Read(ligand_filename)
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/__init__.py", line 51, in Read
    molecules = parser.parse()
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/mol2Parser.py", line 118, in parse
    self.build4LevelsTree({},atmlines)
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/mol2Parser.py", line 372, in build4LevelsTree
    res = self.mol.curChain.get( na )
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 1264, in get
    return self.children.get(function)
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 612, in get
    escapeCharacters=escapeCharacters)
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 162, in select
    newNodes = self.processListItem(nodes, item, sets)
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/protein.py", line 399, in processListItem
    return TreeNodeSetSelector.processListItem(self, nodes, item, sets=sets)
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 217, in processListItem
    newNodes = self.getRange( nodes, item )
  File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/protein.py", line 352, in getRange
    if levItList[0][0]=='#' and levItList[1][0]=='#':
IndexError: string index out of range
00285.nci_2.mol2
setting PYTHONHOME environment
00286.nci_2.mol2



anyone knows what is wrong with this?


--- On Mon, 6/22/09, Sargis Dallakyan <sargis at scripps.edu> wrote:

> From: Sargis Dallakyan <sargis at scripps.edu>
> Subject: Re: ADL: Error loading AutoDock Tools
> To: autodock at scripps.edu
> Date: Monday, June 22, 2009, 1:25 PM
> Hassan Thomas Mamdani wrote:
> > Hi All
> > 
> > I wonder if anyone has encountered the following error
> when loading ADT,
> > and if so what did they do to resolve the issue.
> > 
> > 
> > M:\Notebooks\NB4\04htm53\pH3>adt
> > 
> > M:\Notebooks\NB4\04htm53\pH3>set
> MGLPYTHONPATH=C:\Program Files\MGLTools
> > 1.5.4
> > 
> >
> M:\Notebooks\NB4\04htm53\pH3>"C:\Python25\python.exe"
> "C:\Program
> > Files\MGLTools 1.5.4\MGLTools
> > Pckgs\AutoDockTools\bin\runAdt.py"
> > Run AutoDockTools from C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\AutoDockTools
> > DLL load failed: The specified module could not be
> found.
> > Resource file used to customize PMV:
> M:\\.mgltools\1.5.4\Pmv\_pmvrc
> > Traceback (most recent call last):
> >   File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\AutoDockTools\__init__.py", line
> 373, in
> > runADT
> >     title=title, withShell= not
> interactive, verbose=False)
> >   File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\Pmv\moleculeViewer.py", line 315,
> in __in
> > it__
> >     verbose=verbose,
> trapExceptions=trapExceptions)
> >   File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\ViewerFramework\VF.py", line 345,
> in __in
> > it__
> >     verbose=verbose)
> >   File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\ViewerFramework\VFGUI.py", line
> 270, in _
> > _init__
> >     cnf = {"addScenarioButton":
> False})
> >   File "C:\Program Files\MGLTools
> 1.5.4\MGLToolsPckgs\DejaVu\Viewer.py",
> > line 719, in __init__
> >     master=guiMaster)
> >   File "C:\Program Files\MGLTools
> > 1.5.4\MGLToolsPckgs\DejaVu\ViewerGUI.py", line 433, in
> __init
> > __
> >     self.tvolist =
> TreeView(master=self.ObjectListFrame,displayValue=True)
> >   File "C:\Program Files\MGLTools
> >
> 1.5.4\MGLToolsPckgs\mglutil\gui\BasicWidgets\Tk\TreeWidget\tr
> > ee.py", line 1581, in __init__
> >     self.plus_icon  =
> ImageTk.PhotoImage( master=master,image=plus_icon)
> >   File "C:\Program Files\MGLTools
> 1.5.4\MGLToolsPckgs\PIL\ImageTk.py",
> > line 116, in __init__
> >     self.paste(image)
> >   File "C:\Program Files\MGLTools
> 1.5.4\MGLToolsPckgs\PIL\ImageTk.py",
> > line 181, in paste
> >     import _imagingtk
> > ImportError: DLL load failed: The specified module
> could not be found.
> > hit enter to continue
> > 
> > When I hit enter the splash screen vanishes and the
> program exits.  I'm
> > running on Windows XP and have just seen the error
> after successfully
> > using ADT for a couple of years.  I recently
> changed my own Python
> > installation to ActivePython and have loaded GTK in
> order to use another
> > bit of code.  Would that have anything to do with
> the problem?
> 
> Thank you for your message. We are using Python Imaging
> Library (PIL) 1.1.5 which is a third part package that we
> did not change for a long time: http://www.pythonware.com/products/pil/index.htm
> 
> In order to troubleshoot this problem I'd like to know if
> one of our earlier releases, 1.5.2 for instance, works with
> your current configuration:
> http://mgltools.scripps.edu/downloads/previous-releases/mgltools-1-5.2
> 
> Also, if you use Python 2.5 from python.org instead of
> ActivePython does this problem persists?
> 
> Thank you,
> Sargis
> 
> 
> -- 
> Sargis Dallakyan, Ph.D. - Research Programmer III
> The Scripps Research Institute,
> Dept. Molecular Biology,  MB-5,
> 10550  North Torrey Pines Road,
> La Jolla,  CA 92037-1000
> Tel: (858) 784-9559
> http://mgltools.scripps.edu/Members/sargis
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> 


      


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