On 11/01/16 15:42, Craig James wrote: > It would be helpful if you could be very specific. Are you reading a > file, or creating a molecule via a C++ program? What sort of output are > you looking at, a particular file (like SMILES, SDF, or PDB)? The best > way is to give a concrete example with sample files that will allow > others to repeat your results. Sorry about that. Reading a gaussian log file at http://folding.bmc.uu.se/images/hydronium.log then babel -ig09 hydronium.log -osdf h3o.sdf
In this file only two O-H bonds are made even though the geometry is fine. > > Regards, > Craig > > On Mon, Jan 11, 2016 at 6:02 AM, David van der Spoel > <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote: > > Hi, > > for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB > does detect all bonds. Is this determined by input files (like > bondtyp.txt) or by the code itself? Suggestions for how I can fix it? > > Cheers, > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> > http://folding.bmc.uu.se > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > <mailto:OpenBabel-Devel@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > > > -- > --------------------------------- > Craig A. James > Chief Technology Officer > eMolecules, Inc. > --------------------------------- -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
