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PostPosted: Thu Jan 12, 2017 7:52 pm 
Millimolar User
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Joined: Thu Jan 12, 2017 7:31 pm
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On Windows 7, Open-Source PyMOL 1.8.

After loading the receptor and ligand which were prepared as pdbqt files following the Autodock (2012_ADTtut.pdf) tutorial book and then defining the grid in the PyMOL plugin interface, I am unable to transfer the PyMOL selection under either the receptor or ligand tabs to select the actual receptor or ligand. Seems like it should be a real simple issue and has infact been a problem in both my Ubuntu installation ~2 years ago and now in Windows 7. Also, the starting pdb file never had hydrogens, and had waters and multiple conformers removed.

In both cases the message reads similarly:

C:\Program Files (x86)\MGLTools-1.5.6\Lib\site-packages\AutoDockTools\Utilities24\ -r C:\Python27\lib\site-packages\pymol\pymol_path\.ADplugin\receptor.EcXynA.pdb -o C:\Python27\lib\site-packages\pymol\pymol_path\.ADplugin\receptor.EcXynA.pdbqt -A checkhydrogens

Communication with Dr.Seeliger at the time of the Ubuntu attempt suggested that use of an installer has made the Python script files not executable so permissions were checked with no success. In the current Windows 7 install all the .py files are executable.

I'm sure this is "no brainer" for someone familiar with these programs.

Any guidance would be appreciated.


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