You people at Scripps make great software and give it all freely away for the progress of science, and I really, really appreciate that. I just want you to know, that if you ever have plans to expand upon AutoDock and AD Vina, I and other users would like to see some method of easy atom parameter setup implementation. It would make sense from an end-user point of view, especially with freely available ligand data sets, such as the NCI/NIH Diversity Set.
Thanks, our work is actually taxpayer-funded. We recently proposed something like what you and others are suggesting, but more general, to the NIH funding agency: arbitrary user-supplied scoring functions and atom types for Vina, shareable like spreadsheets. (If you have any questions about this, please contact Prof. Olson, as he's the PI on the NIH proposal)
Please do not email or PM me with questions. Vina.scripps.edu/questions.html
explains where to find help.