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>