autodock41

Usage

Overview

AutoDock perfoms the automated docking of chemical compounds to proteins, i.e. it predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

The AutoDockSuite consists of two main programs of which AutoDock performs the docking of the ligand to a set of grids describing the target protein and AutoGrid pre-calculates these grids.

Options

-p

parameter_filename

-l

log_filename

-o

Use old PDBQ format, charge q in columns 55-61

-k

Keep original residue numbers

-i

Ignore header-checking

-t

Parse the PDBQ file to check torsions, then stop.

-c <

command_file Command mode, by file

-c |

control_program Command mode, by control_program

Examples

On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that directory and unpack (as root) the gzipped map files, then execute AutoDock as shown below:
gunzip *.map.gz
autodock4 -p 1pgp.dpf -l /tmp/1pgp.dlg

The interpretation of results is aided by the AutoDockTools suite. Please also inspect the tutorials offered online.