[Chimera-users] Problem with Gasteiger charges of a formally charged ligand

cdeligka at purdue.edu cdeligka at purdue.edu
Thu Aug 2 12:29:24 PDT 2007

Dear all,

I tried to calculate the Gasteiger charges of peroxynitrite anion using Chimera
(I tried the version that was recently released as well as some previous ones).
This is my PDB file:

HETATM    1  O     2    2        1.225   0.000   1.819
HETATM    2  N     2    2        0.138   0.000   1.281
HETATM    3  O     2    2        0.138   0.000  -0.086
HETATM    4  O     2    2        1.359   0.000  -0.746

The formal charge of this molecule is -1.
For some reason Chimera generates the Gasteiger charges for the molecule but
these charges correspond to a formal charge of zero and not -1.
If I try the other method AM1-BCC the charges that are calculated do correspond
to a formal charge of -1.

In my calculations I do need the Gasteiger charges and so I cannot use the ones
that are calculated by AM1-BCC.

If you have any suggestions please let me know.

Are you aware of any other software that might be able to do this calculation?

Thank you all,


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