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:
HEADER
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,
Christos
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