Dear Egon >That's the German way of writing the term. Is that typo in CDK documentation? I cited from Java_sources/cdk-javadoc-1.0.1/org/openscience/cdk/charges/GasteigerMarsiliP artialCharges.html
>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. Thank you for suggestion. BTW, does somebody make MOE's PEOE_VSA compatible descriptors? Takayuki KOTANI -----Original Message----- From: Egon Willighagen [mailto:[EMAIL PROTECTED] Sent: Sunday, September 09, 2007 10:40 PM To: [EMAIL PROTECTED] Cc: [email protected] Subject: Re: [Cdk-user] Gasteiger charges 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
