Dear Takayuki, On 9/3/07, Takayuki KOTANI <[EMAIL PROTECTED]> wrote: > Gasteiger charges calculated by cdk seems to be different from openbabel's > Gasteiger charges. > It would be the following reasons. > > Cdk tutorial says: > The calculation of the Gasteiger Marsili (PEOE) partial charges is based on > [Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital > electronegative - a rapid access to atomic charges, Tetrahedron, 1980, > 36:3219-3288]. This class only implements the original method which only > applies to σ-bond systems. > > (Tutorial uses "elektronegativity". Is it mistype?)
That's the German way of writing the term. Is that typo in CDK documentation? > Does somebody have an idea which charges is common (normally used one) for > Gasteiger charges? Sigma Gasteiger is more common I think, but should really not be used for compounds which show any kind of delocalization or aromaticity. Use cdk.charges.GasteigerPEPEPartialCharges instead. > And if openbabel's Gasteiger charges is common, how can I calculate its > charges by cdk. I do not know which kind of Gasteiger charges OpenBabel uses. Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
