Autodock plugin
| Type | PyMOL Plugin |
|---|---|
| Download | plugins/autodock_plugin.py |
| Author(s) | Daniel Seeliger |
| License | - |
| This code has been put under version control in the project Pymol-script-repo | |
Description
This plugin should help to set up docking runs with Autodock and view docking results. It has two features:
- Setup of a docking grid for Autodock with PyMOL.
- View the docking results.
Installation
Linux
This plugin is ready "out-of-box" for Linux users through the project Pymol-script-repo
Windows
This plugin is ready "out-of-box" for win users through the project Pymol-script-repo
You can download it manually
- Download plugin
- PyMOL > Plugin > Install Plugin
- MGLTools/AutoDockTools
- AutoDock4.2
- AutoDock Vina
Tutorial Video
Watch Dan Seeliger's autodock plugin tutorial.
Important
- The Autodock tools, does not like funny atoms names like "C1, N13, O28" and so on. Rename them! See example 1.
- Ligands can not be in alternative configuration. Create by: create ROC_A, 1HXB and resn ROC and alt a . See example 2.
Example 1 - Rename of funny atom names
Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7
The example of video http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html
Note, that the module "prepare_ligand4.py" does not like funny names of atoms, so we have to rename them
| Download: examples/autodock_plugin_1.pml | |
| This code has been put under version control in the project Pymol-script-repo | |
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/autodock_plugin_1.pml" highlight="python" />
Open the Autodock/Vina plugin. Check/set the executable to folders (they should be automatically found):
Autodock Tools: /home/you/another/pymol/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24 autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autogrid4 # Platform dependent autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autodock4 # Platform dependent vina executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_vina/autodock_vina_1_1_2_linux_x86/vina # Platform dependent Working Directory: /home/you/another/pymol/workingdir
Enlarge the window and click Save Plugin Configuration file. Plugin will not work, if you do not save.
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.
Click cdk2 to the "right", and see where the files are located.
Click tab Ligands. Mark EFP, and click EFP in the Ligand list. Here is the files stored. Click Generate Ligand
Click tab Docking, and click Run Vina. Wait 3-5 minutes, until Writing output ... done.
Click tab View poses, Browse to EFP.docked.pdbqt. Click Load, Show best 10. Experiment with "Display options, and click the candidates"
Congratulations, you did it!
Example 2 - Alternative configurations of a Ligand
Read about the protein here: http://www.proteopedia.org/wiki/index.php/1hxb
Ligands can not be in alternative configuration. Create by: create ROC_A, 1HXB and resn ROC and alt a .
| Download: examples/autodock_plugin_2.pml | |
| This code has been put under version control in the project Pymol-script-repo | |
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/autodock_plugin_2.pml" highlight="python" />
References and LICENSES
Vina
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
MGLTOOLS
LICENSE of MGLTOOLS:
This software is copyrighted by Michel F. Sanner (sanner@scripps.edu) and TSRI.
The following terms apply to all files associated with the software
unless explicitly disclaimed in individual files.
MGLTOOLS SOFTWARE LICENSE AGREEMENT.
1. Grant Of Limited License; Software Use Restrictions. The programs
received by you will be used only for NON COMMERCIAL purposes.
This license is issued to you as an individual.
For COMMERCIAL use done with the software please contact Michel F.
Sanner for details about commercial usage license agreements.
For any question regarding license agreements, please contact
Michel Sanner:
TSRI, Molecular Biology Department, TCP 26,
10550 North Torrey Pines Road, La Jolla, CA 92037
sanner@scripps.edu
tel (858) 784-7742
fax (858) 784-2341
2. COMMERCIAL USAGE is defined as revenues generating activities. These
include using this software for consulting activities and selling
applications built on top of, or using this software. Scientific
research in an academic environment and teaching are considered
NON COMMERCIAL.
3. Copying Restrictions. You will not sell or otherwise distribute commercially
these programs or derivatives to any other party, whether with or without
consideration.
4. Ownership of Software. You will not obtain, and will not attempt to
obtain copyright coverage thereon without the express purpose written
consent of The Scripps Research Institute and Dr. Sanner.
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