"-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill valencies, but rather converrts implicit to explicit hydrogens. You can open in Avogadro and click "Build/AddHydrogens" to do this.
Could I ask you where the XYZ file came from? It may be that a different route might help. Note to Geoff: would this be a useful 'op' or else option on XYZ? - Noel On 12 June 2017 at 16:22, Christopher Beeler <cbee...@dal.ca> wrote: > Hello, I am currently trying to use OpenBabel to add hydrogen to my XYZ > molecules but it is not adding any. I am using version 2.3.2 on Linux. I > have attached the input and output files. The command I am using is 'babel > -ixyz molecule_1.xyz -oxyz molecule_1.in -h'. The output file should have 8 > hydrogen now but it still contains 0. > > > Thank you-Chris Beeler, cbee...@dal.ca > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
