Hi all,
Please imagine this to be a brand new machine with the latest installation of:
Autodock Vina
Autodock
AutodockTools (MGLTools).
I'm following a Nature Protocol for the prediction of activation sites with AutoLigand. This is the first time I've run AutoGrid on my machine, that's important to consider.
I've set up my macromolecule, assigned hydrogens, assigned Kollman charges, saved as a pdbqt, assigned grid map types, and finally defined the gridbox.
The protocol states that I must "Run AutoGrid at the command line". It can also be performed inside AutoDockTools by selecting Run->AutoGrid. However, when I do this I get the following error (please see below):
I was disappointed to learn the autodocktools executes Python. And from the output of the error quite an old version of python too. Any idea what on earth is going on and how to correct this?
Python 2.7.11 (v2.7.11:6d1b6a68f775, Dec 5 2015, 20:32:19) [MSC v.1500 32 bit (Intel)] on win32
Type "copyright", "credits" or "license()" for more information.
==== No Subprocess ====
>>> {'gui': None, 'cmd': , 'name': 'select'}
{'gui': None, 'cmd': , 'name': 'deselect'}
{'gui': , 'cmd': , 'name': 'clearSelection'}
{'gui': None, 'cmd': , 'name': 'expandSelection'}
{'gui': None, 'cmd': , 'name': 'selectAround'}
{'gui': , 'cmd': , 'name': 'saveSet'}
{'gui': None, 'cmd': , 'name': 'createSetIfNeeded'}
{'gui': , 'cmd': , 'name': 'invertSelection'}
{'gui': , 'cmd': , 'name': 'selectSet'}
{'gui': , 'cmd': , 'name': 'selectFromString'}
{'gui': , 'cmd': , 'name': 'directSelect'}
{'gui': , 'cmd': , 'name': 'selectInSphere'}
{'gui': , 'cmd': , 'name': 'selectHeteroAtoms'}
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\lib-tk\Tkinter.py", line 1410, in __call__
return self.func(*args)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\Pmv\guiTools.py", line 353, in do_1
self.kill(e.widget.get(e.widget.nearest(e.y)))
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autostartCommands.py", line 144, in kill
if self.manager.processCts[prog]>0:
KeyError: 'Program'
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\lib-tk\Tkinter.py", line 1410, in __call__
return self.func(*args)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\Pmv\guiTools.py", line 353, in do_1
self.kill(e.widget.get(e.widget.nearest(e.y)))
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autostartCommands.py", line 144, in kill
if self.manager.processCts[prog]>0:
KeyError: 'Program'
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\lib-tk\Tkinter.py", line 1410, in __call__
return self.func(*args)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\Pmv\guiTools.py", line 353, in do_1
self.kill(e.widget.get(e.widget.nearest(e.y)))
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autostartCommands.py", line 144, in kill
if self.manager.processCts[prog]>0:
KeyError: 'Program'
Resolved.
The age old classic of white space in paths e.g., "Program Files (x86)".
That's actually great. One more suggestion, never perform dockings in C: drive. Please make a new workpath and execute the commands in some other drive to avoid many permission errors as well as disk space issues when you perform long run dockings
Anthony Nash you can follow this tutorial: https://www.youtube.com/watch?v=k6tqCeDIwEk
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