Hi Christos, The Gasteiger implementation in Antechamber (which Chimera uses for partial-charge calculation) ignores the formal charge specification -- which is a bug that I believed I've reported to the Antechamber developers at least once but I guess I'll report it again. If you must use Gasteiger charges, at least some of the alternatives include the PETRA server run by the Gasteiger group itself: http://www2.chemie.uni-erlangen.de/services/petra/index.html and OpenBabel: http://openbabel.sourceforge.net/wiki/Capabilities --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Aug 2, 2007, at 12:29 PM, cdeligka@purdue.edu wrote:

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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