Overview

    The first phase of an AutoDock experiment involves using AutoGrid to precalculate the energy of a specific 'probe' atom at regular points over a 3D space around the receptor. These energies are saved in 'grid maps'.  There is one grid map for each atom type in the ligand plus an electrostatics map and a desolvation map. The grid parameter file specifies the 3D search space by setting the number of points in each dimension, the center of the grids and the spacing between points. It also specifies the types of probe atoms to use, the filename of the receptor and the names of each the output gridmaps. The grid parameter file can be prepared interatively using AutoDockTools (ADT) or with prepare_gpf4.py, a python script which can be found in AutoDockTools/Utilities24.  Typing the name of a script in that directory at a shell prompt results in printing Usage: which is an overview of how to use the script.

Usage

prepare_gpf4.py -l pdbqt_file -r pdbqt_file

    Description of command...
        -l ligand_filename
        -r receptor_filename

    Optional parameters:
        [-i reference_gpf_filename]
        [-o output_gpf_filename]
        [-p parameter=newvalue]
        [-d directory of ligands to use to set types]

Procedure

1. Install MGLTools if you have not already done so.  This will install the graphical user interface and the Python shell scripts for ADT (AutoDockTools).  Where MGLTools is installed depends on which platform you are using.  See this FAQ on the MGLTools web site for more information about installation locations on different platforms.  Briefly, you can find "pythonsh" in:

• Linux: "$MGL_ROOT/share/bin", where $MGL_ROOT is either "/usr/local/MGLTools" (if you installed as 'root') or "$HOME/MGLTools" (if you installed as 'your_username').
• Mac OS X: /Library/MGLTools/share/bin
• Windows: Cut-and-paste this:

SET PYTHONPATH=C:\Python24\Lib\site-packages\MGLTools\;C:\Python24\Lib\site-packages\MGLTools\PIL;C:\Python24\Lib\site-packages\MGLTools\Numeric
C:\Python24\python.exe prepare_ligand.py