We present a set of auxiliary programs for molecular mechanics studies on a wide class of organic molecules. This software package is devoted to solve the following problems: (1) identifying bond and atom types; (2) judging atomic equivalence; (3) generating residue topology files; and (4) finding missing force field parameters and supplying reasonable suggestions. As an accessory module in the AMBER 7 and AMBER 8 packages, antechamber can generate input automatically for most organic molecules in a database. The algorithms behind these manipulations are presented here, and may be useful outside the Amber family of programs as well.