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

[Eric Pettersen]

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 at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu


On Aug 2, 2007, at 12:29 PM, cdeligka at 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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