Dear Takayuki, May be you can take a look a this cdk article 3.3 from 2006
http://sourceforge.net/project/showfiles.php?group_id=20024&package_id=124796 >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? Gasteiger calculated the total charges meaning the sum of pi-charges and sigma-charges. But you can find more explanation in the article. > >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. Best resguards, Miquel -- Miguel Rojas Cherto Netherlands Metabolomics Centre (NMC) Leiden University Einsteinweg 55 NL-2333 CC Leiden tel (direct): +31 715276327 mail: [EMAIL PROTECTED] ------------------------------------------------------------------------- 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
