Hi, When adding partial charges (AM1-BCC) to small molecules in chimera, we observed that atoms in symmetrical groups are not assigned the same partial charge. Specifically, the two oxygens in a carboxyl group are not assigned the same partial charge. See excerpt from mol2 file below: carboxyl: 20 C20 23.4850 19.6920 64.8870 C.2 1 BCZ 0.9226 21 O21 22.2660 19.7760 65.0340 O.co2 1 BCZ -0.9253 22 O22 24.2040 20.8120 64.7970 O.co2 1 BCZ -0.7643 There is a significant difference in partial charge between the two carboxyl oxygens (0.161). This problem was observed in both older (with mopac) and newer (with sqm) versions of chimera. The molecule is peramivir from the pdb1L7F crystal structure. Similar problems were observed for other molecules that inhibit Neuraminidase for example those 1L__ pdb structures. This problem is also observed when assigning am1bcc charges to the mol2 file using antechamber/sqm directly. Best Regards, Brian Fochtman, Trent Balius, Sudipto Mukherjee