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How to prepare a docking parameter file for AutoDock4

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

This How-to addresses using the python script 'prepare_dpf4.py' to create a docking parameter file for AutoDock4. This docking parameter file specifies the ligand to move during the search, the gridmap files to use for the energy evaluations, which search algorithm to use and parameters for it as well as how many separate docking runs to perform and how many energy evaluations to use in each run. (NOTE: You must have installed MGLTools).

Overview

An AutoDock experiment involves searching for the lowest energy state of the ligand-receptor complex. AutoDock implements four different search algorithms: simulated annealing(SA), genetic algorithm(GA), local search(LS) and a hybrid global-local Lamarkian GA(LGA or GALS). The parameters specifying which algorithm to use along with others specifying the extent of the calculation are contained in a docking parameter file. The docking parameter file can be prepared interatively using AutoDockTools (ADT) or with prepare_dpf4.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_dpf4.py -l pdbqt_file -r pdbqt_file

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

Optional parameters:
[-o output_gpf_filename]
[-i template dpf_filename]
[-p parameter_name=new_value]
[-k list of parameters to write]

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_dpf4.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_dpf4.py -l ligand_filename -r receptor_filename [options]

Input

The required input for this script are (1) the name of the file containing the formatted ligand and (2) that of file containing the formatted receptor. They must be in pdbqt format for AutoDock4.

Output

The output from this script is a docking parameter file, typically ligand_receptor.dpf.

Options

1. -i: reference_dpf_filename
A template docking parameter file can be specified which will be used to set docking parameters.
2. -o: output_dpf_filename
The default output filename is 'ligandname_receptorname.dpf'.
3. -p: parameter=value
Specific parameters can be set using this option.
4. -k: list of parameters to write
Different algorithms are invoked with different sets of parameters.

Known problems

None so far...


by Ruth Huey last modified 2007-08-27 14:21

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