ADL: vina virtual screening result?

venkat vkabas at yahoo.com
Tue Jun 23 12:36:18 PDT 2009


Hey 

I did run vina for virtual screening.

Is it any script that can be useful extract the best result pdbqt.
Other words, any way to check quickly which ligand has lowest
binding energy and how can I get pdbqt from entire data base of ligand pdbqt.

Thanks
venkat

--- 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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