Autodock plugin

Description

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.

Installation

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.

Author

Daniel Seeliger

Example

The example of video http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html

reinitialize 

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
cmd.disable("binding_site")
hide sticks, binding_site

Click tab Receptor. Mark cdk, and click Generate Receptor.

References

If you used AutoDock Vina in your work, please cite:
O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461