ADL: Best way to assign partial charges

Douglas Houston dhouston at
Thu Apr 16 08:51:39 PDT 2009

I've tried to find out as much as I can about the best way to assign partial charges to the receptor, but I've only succeeded in making myself more confused.

According to the manual, "appropriate partial atomic charges must be assigned. This can be achieved by
the user’s preferred method, e.g. using InsightII, Quanta, Sybyl, AMBER or CHARMm. Alter-
natively, one of the shell scripts described in the Appendix can be used."

According to the FAQ on the website, "the AD4 scoring function was calibrated using Gasteiger partial charges on both the ligand and the macromolecule."

But according to the front page of the website "AutoDock 4.0 now has a free-energy scoring function that is based on ... the AMBER force field"

So can anyone answer the following questions:

1. Does the scoring function use Gasteiger charges or the AMBER force field?

2. Was AD4 calibrated using Gasteiger charges assigned by the script? If not, how exactly were they assigned?

3, Is there an "official" recommended way of assigning charges to the receptor before calculating grids, and if so, what is it?

Any help would be appreciated,


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