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Autodock plugin

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Revision as of 16:45, 4 December 2011 by Tlinnet (talk | contribs) (→‎Example)
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This plugin should help to set up docking runs with Autodock and view docking results. It has two features:

  1. Setup of a docking grid for Autodock with PyMOL.
  2. View the docking results.


you can download it manually

  1. Download plugin
  2. PyMOL > Plugin > Install Plugin
  3. MGLTools/AutoDockTools
  4. AutoDock4.2
  5. AutoDock Vina

Tutorial Video

Watch Dan Seeliger's autodock plugin tutorial.


Daniel Seeliger


The example of video


fetch 3IG7, async=0
hide everything, all
create cdk2, 3IG7 and polymer
create EFP, 3IG7 and organic
delete 3IG7
show_as cartoon, cdk2
show_as sticks, EFP
util.cbay EFP

Open the Autodock/Vina plugin. Set executable to folders:

Autodock Tools: /home/dseelig/lib/python2.5/site-packages/AutoDockTools/Utilities24
autogrid4 executable: /home/dseelig/ADT_bin/autogrid4
autogrid4 executable: /home/dseelig/ADT_bin/autodock4
vina executable: /home/dseelig/vina/vina

Enlarge the window and click Save Plugin Configuration file.

Click tab Grid settings. In Calculate Grid Center by Selection, write EFP.
Try clicking Wired Box in top right, and then Show Box, Hide Box, Cylindric Box, Show Box.
Then push Select binding site. In PyMOL, write

show sticks, binding_site