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