Follow the "Download Files" link on the upper right and select "PDB File (Text)", save this somewhere convenient.
Using Notepad or your favorite text editor create two new files, named protein.pdb and ligand.pdb
Open the PDB file you downloaded with the text editor and highlight, copy, and paste the protein atoms into the protein.pdb file you just created. Highlight, copy, and paste the ligand atoms into the ligand.pdb file as well. NOTE(1)If you have Cl, or Z atoms these can be ignored. NOTE(2)If you have a multimeric structure you should determine which chain and ligand you need first by visual examination while at pdb.org
Go to http://davapc1.bioch.dundee.ac.uk/prodrg/index.html and highlight, copy and paste the contents of the ligand.pdb file you created in step 4 into the text box just under "Paste your input here (PDB coordinates, MDL MOLfile, text drawing). See below for instructions."
Select "Chirality Yes", "Full charges Yes", "Energy minimization No" and then "Run PRODRG".
Scroll down to "Docking / MD simulations" and click on the "AUTODOCK PDBQ file version 3.0 link".
Highlight the contents in the text box and copy them to a new text file. Call this ligand.pdbq