Before You Start AutoDock 3

You need AutoGrid 3 grid maps that have been computed for the receptor you want to dock to.

AutoGrid 3

To run AutoGrid 3, you need:

• a grid parameter file, or GPF; let's say it is called my_receptor.gpf
• a receptor file in PDBQS format--the receptor can be a protein, DNA, RNA or other macromolecule.

Once you have these files, you can type the following at the command line:

     autogrid3 -p my_receptor.gpf -l my_receptor.glg &

AutoGrid 3 uses the following flags:

• -p specifies the name of the GPF (grid parameter file) that will be read in by AutoGrid 3
• -l specifies the name of the GLG (grid log file) that will be created by AutoGrid 3

AutoDock 3

Before you can start AutoDock 3, you need:

• a docking parameter file, or DPF; let's say it is called my_docking.dpf
• a ligand saved as a PDBQ file
• a set of grid maps calculated by AutoGrid 3; this includes:
  • the map files (extension ".map")
  • the grid size file (extension ".xyz")
  • the grid field file (extension ".fld")

Once you have these files, you can type the following at the command line:

     autodock3 -p my_docking.dpf -l my_docking.dlg &

Take a look at the AutoDock 3 User's Guide for more details.