This page describes the process of creating a PDBQT file for a rigid receptor starting from a PDB file. The resulting PDBQT can be used as an input for AGFR, ADFR and ADCP, as well as AutoDock4 and Autodock Vina.
When docking ligands it is usually better to use the biologically active molecule or biological assembly, which in some cases is different from the asymmetric unit provided by a PDB file. You can download the biological assembly from the PDB website under the “Download Files” pull down menu on the web page of the PDB entry you are interested in. Alternatively it can be built from header information in the PDB file. For this example we went to the PDB web site and searched for 4EK3 and downloaded the bioloigcal assembly which was saved as 4ek3.pdb1 in our download folder.
The next step is to add hydrogen atoms. While the prepare_receptor program provided in the ADFRsuite is capable of adding hydrogen atoms using OpenBabel, we found that the program reduce from the Richardson lab. tends to provide better results. Reduce is also included in the ADFRsuite and is readily available. Reduce is run from the command line as shown below. Note: on Windows the ADFRSuite/bin path is added automatically to the path so you can type reduce directly into a windows command prompt window that you can open by typing cmd after clicking on the start menu button.
$ADFRsuite_INSTALL_DIR/bin/reduce ~/Download/4ek3.pdb1 > 4ek3H.pdb
Next we use the prepare_receptor program from the ADFRsuite to generate a PDBQT file.
$ADFRsuite_INSTALL_DIR/bin/prepare_receptor -r 4ek3H.pdb -o 4ek3.pdbqt
Voila ! you should have a usable PDBQT file for your receptor.