From Jan-Christoph Westermann:
Documentation of the pdbq format is somewhat inconclusive. PDBQ is
essentially a modification of the pdb format to store partial charges.
A short explanation of pdbq is given in the AutoDock online manual:
http://www.scripps.edu/mb/olson/gmm/autodock/ad305/
Using_AutoDock_305.21.html#pgfId=29703