Hi Christos, Please, can you tell us if you're using the tag "--partialcharge gasteiger" or not, in your calculation?
I was having the same problem with many charged molecules. I noticed that if you do NOT use that tag, obabel correctly calculate the partial charges. For example if you're calculating the charges for a molecule charged +2, the sum of all the atomic partial charges should be +2. Please, can you say if that works in your case? Gio 2012/3/15, Christos Deligkaris <deligka...@gmail.com>: > Dear OpenBabel users, > > I am using OpenBabel to calculate the Gasteiger partial charges of a > positively charged molecule (net formal charge of +2). > > The partial charges OpenBabel calculates result in a net charge of 0. Is it > possible to specify somehow the formal charge of the molecule for > OpenBabel? > > Thank you, > > -- > Christos > ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
