At the moment, the Avogadro (and Open Babel) code has a heuristic to minimize collinear atoms and 180° dihedrals. If you'd like to suggest another heuristic, we can probably work on it.
Right now, the z-matrix code also won't create dummy atoms, and this may be needed to reconcile your molecule. Without seeing the entire molecule (e.g., Cartesian geometry) I don't have the faintest idea how to solve your problem, other than to put into the code an if/else to look for reuse of angle/dihedral atom definitions. Alternatively, is there another open source program which gives you a satisfactory z-matrix? Thanks, -Geoff On Aug 29, 2011, at 4:25 PM, David Condon wrote: > Hello all, > > I am trying to create Gaussian Z matrices for my work. > > However, there are issues in the output from Avogadro. For example, > > H 5 r6 4 a6 1 d6 > H 5 r7 4 a7 1 d7 > C 5 r8 4 a8 1 d8 > > atoms 5, 4, and 1 appear 3 times. This means that that torsion cannot be > scanned in Gaussian because it isn't properly defined. > > Open Babel has the same problem when I convert an xyz file from Avoagadro to > gzmat. ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
