That XYZ file does not represent ethanol. It describes some sort of radical species involving C-C-O. The XYZ format does not have an implicit valence model - if the atoms are present, they are in the file - if not, they don't exist.
You may be confusing this with a MOL file which has an implicit valence model and a way of describing the formal charge on each atom (how do we know how many hydrogens to add otherwise?). If interested, you can read more about these issues at http://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/ Regards, Noel On 5 April 2015 at 15:46, eric henon <eric.he...@univ-reims.fr> wrote: > Hello, > > I' m using open babel (2.3.1 on Mac Os and I tried also 2.2.3 on a Linux > machine) > to add hydrogen atoms on a ligand, and it does not work. > > The command I entered is: > > babel -iXYZ ligand.xyz -oXYZ ligandH.xyz -h > > as specified in the "help" list. > > The generated file is exactly the same as the input file, > ... without any hydrogen atoms added. > > Then, I tried on a very simple case: > > 3 > ethanol "backbone" > C 0.00000 0.00000 0.00000 > C -0.68400 -1.18400 -0.48300 > O -0.02400 -2.32700 -0.01700 > > It does not work either (either on Mac OS or a Linux machine). > > I probably missed something when using openbabel. > Any help will be appreciated. > Thanks. > > Ric > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, > sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for > all > things parallel software development, from weekly thought leadership blogs > to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
