[Chimera-users] Asymmetric partial charges on symmetric atoms

Brian Fochtman brianfochtman at gmail.com
Fri May 27 08:48:26 PDT 2011


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:

     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
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