Molecule conversions are a crucial point of AutoDock computations. AutoDock uses PDB format as its base but it cannot make calculations with PDB. AutoDock needs to convert PDB files into PDBQT files. Thankfully it comes with a free AutoDockTools app and if you are lucky, it is easy to make conversions. AutoDock package could drive you crazy while you are trying to make conversions or create configuration files but there are not any other options.
As I said, the app we need to use is AutoDockTools and it is a part of MGLTools (Molecular Graphics Laboratory Tools) software. Download and install it. Even though I usually work on Mac and Linux I was not able to install MGLTools into any of my UNIX based (Mac or Linux) machines. Mostly the Python version is the problem. MGLTools requires an archaic version of the Python Programming Language. UNIX based systems generally use Python extensively so it is hard to change the system default for MGLTools.
I started my Windows machine and install the Windows version. Installation is pretty straightforward. Just click Next, Next, Next and it is ready to use. The installation wizard will start Python Molecule Viewer at the end but you do not need that. You have to start AutoDockTools via Start menu or the Desktop icon.
After launching the app, you can directly try to open your PDB molecule. File > Read Molecule.
The molecule will be visible on the main window. Edit > Charges > Compute Gasteiger
The resulting warning may be discouraging. But do not worry.
Just click OK and continue with; Grid > Macromolecule > Choose
You will be prompt with the next screen:
Pay attention to the saving address. You have to write the full address of the path including the filename and the extension.
In the end, if you have not experienced any other error you will have a new pdbqt file of your macromolecule.
NEXT: Converting the ligand molecule into PDBQT