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PostPosted: Thu Jan 12, 2017 11:33 am 
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Joined: Thu Jan 12, 2017 11:29 am
Posts: 1
Hi,

I am trying to use Malonyl-CoA (based on chemspider id 10213 and converted to pdb by pymol) as ligand for a docking run (following this tutorial http://vina.scripps.edu/tutorial.html). If I click on "ligand" => "torsion tree" => "choose torsion" I get the following error:

Code:
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 ====
>>> adding gasteiger charges to  receptor_1t1u_1_A_r161_764
Sorry, there are no Gasteiger parameters available for atom Malonyl_CoA_chemspider_10213: :UNK:O
Sorry, there are no Gasteiger parameters available for atom Malonyl_CoA_chemspider_10213: :UNK:O
Sorry, there are no Gasteiger parameters available for atom Malonyl_CoA_chemspider_10213: :UNK:O
Sorry, there are no Gasteiger parameters available for atom Malonyl_CoA_chemspider_10213: :UNK:O
no secondary structure set for chain:   !
no secondary structure set for chain:   !
no secondary structure set for chain:   !
no secondary structure set for chain:   !
no secondary structure set for chain:   !
no secondary structure set for chain:   !
no secondary structure set for chain:   !
no secondary structure set for chain:   !
Exception in Tkinter callback
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 1403, in __call__
    return self.func(*args)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\mglutil\util\callback.py", line 86, in __call__
    return apply(self.function, args, kw)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\Pmv\dashboard.py", line 1953, in handleRadioButtons
    self.menu.delete('All')
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 2662, in delete
    self.tk.call(self._w, 'delete', index1, index2)
TclError: bad menu entry index "All"
no secondary structure set for chain:   !
no secondary structure set for chain:   !


any ideas?

Thanks!


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