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Difference between revisions of "Autodock plugin"

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== Example ==
 
== Example ==
 +
The example of video http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html
 
<syntaxhighlight lang="python">
 
<syntaxhighlight lang="python">
 
reinitialize  
 
reinitialize  
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util.cbay EFP
 
util.cbay EFP
 
</syntaxhighlight>
 
</syntaxhighlight>
 +
Set executable to folder:
 +
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'''
 
[[Category:Plugins]]
 
[[Category:Plugins]]

Revision as of 16:34, 4 December 2011

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

Set executable to folder:

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