Daniel Seeliger

Pic 1

News:

The pmx(pymacs) project now lives here:
http://code.google.com/p/pmx/

more software

Welcome to the new Autodock/Vina plugin for PyMOL.
It contains a bunch of new features such as
  • Defining binding sites and export to Autodock and VINA input files
  • Doing receptor and ligand preparation automatically
  • Starting docking runs with Autodock or VINA from within the plugin
  • Viewing grid maps generated by autogrid in PyMOL
  • Handling multiple ligands and set up virtual screenings
  • Set up docking runs with flexible sidechains
  • To get a first idea on how to use the plugin, watch the basic tutorial,
    learn how to set up a virtual screening with the virtual screening tutorial,
    see how you can deal with grid maps with the grid map tutorial,
    and get an idea about docking runs with flexible sidechain with the flexible sidechains tutorial.


    Download plugin here: autodock.py

    SOME NOTES:

    The plugin is developed and tested on Linux. I have no other possibilities to test it and to fix bugs related to other operating systems. However, if you use the plugin on a Mac and experience some errors when scripts from the MGLTools package are executed, try to replace the first line in these scripts.
     #!/usr/bin/env python 
    should be replaced by
     #!/usr/bin/env /Library/MGLTools/1.5.4/bin/pythonsh
    ( note the whitespace between env and /Library )

    The scripts executed by the plugin are:
  • prepare_receptor4.py
  • prepare_flexreceptor4.py
  • prepare_ligand4.py
  • prepare_gpf4.py
  • prepare_dpf4.py


  • I sometimes experienced crashes (segmentation faults) when executing autogrid or autodock. This is due to redirecting the log file output to the plugin text viewer window. You can switch this feature off by setting the environmental variable "ADPLUGIN_NO_OUTPUT_REDIRECT".

    Ligand names should not contain an underscore, e.g. ligand_1.pdb, rename it to ligand-1.pdb.

    Happy Docking!