Some of the automated scripts will remove non-protein components, but you can use the GUI to process coordinates to create a PDBQT file. The coordinates are input, hydrogens added, and charges calculated using the menus in the PMV portion of the GUI. This process is described in more detail in the tutorial. Note that the current Babel-based method for adding hydrogens will not optimize the position of the hydrogens and often makes mistakes in hydrogen placement for non-protein molecules--it is often better to add these hydrogens manually using an external molecular modeling program.