Hi, <br><br>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:<br>

<br>carboxyl:<br>     20 C20        23.4850   19.6920   64.8870 C.2        1 BCZ    0.9226<br>     21 O21        22.2660   19.7760   65.0340 O.co2     1 BCZ   -0.9253<br>     22 O22        24.2040   20.8120   64.7970 O.co2     1 BCZ   -0.7643<br>

<br>There is a significant difference in partial charge between the two carboxyl oxygens (0.161).  <br><br>This problem was observed in both older (with mopac) and newer (with sqm) versions of chimera.<br><br>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. <br>

<br>This problem is also observed when assigning am1bcc charges to the mol2 file using antechamber/sqm directly. <br><br>Best Regards,<br><br>Brian Fochtman,<br>Trent Balius,<br>Sudipto Mukherjee<br><br><br>