Autodock Download For Windows

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AutoDock 4.2.6 Download Page AutoDock is now distributed freely under the GNU GPL for all to use. If you plan to use AutoDock for commercial purposes we encourage donations to the Olson Laboratory to help support further development of the AutoDock suite of programs. OS Files Installation. AutoDock Vina AutoDock Vina is an open-source program for doing molecular docking. It was originally designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab (now CCSB) at The Scripps Research Institute. The latest version of AutoDock Vina is v.1.2.0. AutoDock Vina is.

TypePyMOL Plugin
Downloadplugins/autodock_plugin.py
Author(s)Daniel Seeliger
License-
This code has been put under version control in the project Pymol-script-repo
  • 2Installation
  • 7References and LICENSES

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

Linux

This plugin is ready 'out-of-box' for Linux users through the projectPymol-script-repo

Autodock Download For Windows

Windows

This plugin is ready 'out-of-box' for win users through the projectPymol-script-repo

You can download it manually

  1. Download plugin
  2. PyMOL > Plugin > Install Plugin

Tutorial Video

Watch Dan Seeliger's autodock plugin tutorial.

Autodock download for windows 10

Important

  1. The Autodock tools, does not like funny atoms names like 'C1, N13, O28' and so on. Rename them! See example 1.
  2. 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

Open the Autodock/Vina plugin. Check/set the executable to folders (they should be automatically found):

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

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 .

Autodock Download For Windows 7 64 Bit

Download: examples/autodock_plugin_2.pml
This code has been put under version control in the project Pymol-script-repo

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:

Autodock Vina Download For Windows 10

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