ADL: AutoDock Vina Viewing Results

Nancy nancy5villa at gmail.com
Sun Oct 11 14:41:51 PDT 2009


Hello,

After a docking run using Vina, when I try to view the results in
AutoDockTools by clicking on "Analyze -> Dockings -> Open AutoDock vina
result..." and I choose "Single molecule with multiple conformations", I
receive the following error message (from the python shell):

=====================================================

>>> ERROR *********************************************
Traceback (most recent call last):
  File
"/usr/local/MGLTools-1.5.4/MGLToolsPckgs/Updates/tested/ViewerFramework/VF.py",
line 735, in tryto
    result = apply( command, args, kw )
TypeError: doit() got an unexpected keyword argument 'modelsAs'
ERROR *********************************************
Traceback (most recent call last):
  File
"/usr/local/MGLTools-1.5.4/MGLToolsPckgs/Updates/tested/ViewerFramework/VF.py",
line 735, in tryto
    result = apply( command, args, kw )
  File
"/usr/local/MGLTools-1.5.4/MGLToolsPckgs/Updates/tested/AutoDockTools/autoanalyzeCommands.py",
line 3061, in doit
    mols.current_index = 0
AttributeError: 'str' object has no attribute 'current_index'

=====================================================


Also, as another question, I have used the FlexX program for docking before,
and it takes less than a minute to dock a compound on a single CPU; does
AutoDock/Vina perform docking in a more comprehensive manner, thus taking
more time?  Is there any particular single computer/small cluster hardware
configuration setup that is optimal for running AutoDock/Vina (is there any
way to accelerate Vina on a GPU as well)?

Thanks,

Nancy


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