To convert .pdbqt to .pdb, just the last two columns in the file need to be deleted. Its apparently simple on a *NIX machine but not windows. Its easy to automate I hope.
To convert from PDBQT format to PDB format, the simplest thing to do is to remove the charge (Q) and atom type (T) columns; this can be achieved using a simple UNIX command. Make sure you are in the same directory where you created my_docking.pdbqt, and type:
cut -c-66 my_docking.pdbqt > my_docking.pdb