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How to prepare a grid parameter file for AutoGrid 4

This How-to applies to: AutoDock 4
This How-to is intended for: User

This How-to addresses using the python script 'prepare_gpf4.py' to create a grid parameter file for AutoGrid4. This 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. (NOTE: You must have installed MGLTools).

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]
[-x flexres_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). See also: How to setup ADT scripts.

2. In your working directory either copy 'prepare_gpf4.py' from "MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24", or make sure your path includes 'local_install', the directory where MGLTools is installed locally.
yourpath = local_install/MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24

3. Run the script at the command prompt using the "pythonsh" script with the desired flags and arguments:
    pythonsh [yourpath or .]/prepare_gpf4.py -l ligand_filename -r receptor_filename [options]

Input

The required input for this script are the names of the file containing the formatted ligand and that of file containing the formatted receptor. They must be in pdbqt format for AutoGrid 4.

Output

The output from this script is a grid parameter file, typically receptor_name.gpf.

Options

1. -i: reference_gpf_filename
A template grid parameter file can be specified which will be used to set the location and extent of the gridmaps.
2. -o: output_gpf_filename
The default output filename is the name of the receptor + .gpf.
3. -p: parameter=value
Specific parameters can be set using this option.
4. -d: directory of ligands to use to set types
All pdbqt files in the specified directory will be read to obtain a list used to set ligand_types in the gpf.

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_gpf4.py

Known problems

To specify coordinates for the parameters gridcenter or npts, it is necessary to use a reference gpf file containing the desired values:
prepare_gpf4.py -l ind.pdbqt -r hsg1.pdbqt -i reference.gpf -o test.gpf

by Ruth Huey last modified 2010-05-18 13:40

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