On 2012-10-08 14:45, David van der Spoel wrote: > On 2012-10-08 10:55, David van der Spoel wrote: >> Hi, >> > To answer my own question: I now installed trunk, the development > version. The gaussian files now work fine, but the fulvene.pdb file > still gives problems: > > % babel --version > No output file or format spec! > Open Babel 2.3.2 -- Oct 8 2012 -- 14:31:48 > > % babel -ipdb fulvene.pdb -oinchi ---errorlevel 2 > ============================== > *** Open Babel Information in NewPerceiveKekuleBonds > Kekulize: Huckel rule not satisfied for molecule fulvene.pdb > > ============================== > *** Open Babel Information in NewPerceiveKekuleBonds > Kekulize: Huckel rule not satisfied for molecule fulvene.pdb > Kekulize: Cannot get an even number of electron for molecule fulvene.pdb > > InChI=1S/C6H8/c1-6-4-2-3-5-6/h2-4H,5H2,1H3 > > It adds TWO H for InChi output, not for SDF output, but it only produces > two double bonds (out of three). I guess these are related? > > Thanks for reading, > Sorry for spamming but I have to correct this, the gaussian files produce the right inchi but not the correct bondorder!
% wget http://folding.bmc.uu.se/fulvene-g4.log.gz % babel -ig09 fulvene-g4.log.gz -osdf fulvene.sdf % open fulvene.sdf (in Avogadro) Look at the bonds. -- 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 ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
