See the docs: "When aligning molecules, the atoms of the two molecules must be in the same order for the results to be sensible."
Try rearranging the atoms into canonical order first: obabel C:\Users\noel\Desktop\conf1.mol2 -O tmp.mol2 --canonical obabel C:\Users\noel\Desktop\conf2.mol2 -O tmp2.mol2 --canonical - Noel On 16 October 2012 16:23, scott_m <js...@cam.ac.uk> wrote: > Dear all, > > I have been using OBAlign() to get rmsd values between conformers but just > came across an erroneous value of 3.14 for the molecule N-Acryloyl glycine, > the CSD function tormat gives a rmsd of 0 for the two conformers. Any idea > what is going wrong here? I've attached the two mol2 files. > > Thanks, > > Scott > conf1.mol2 <http://forums.openbabel.org/file/n4655579/conf1.mol2> > conf2.mol2 <http://forums.openbabel.org/file/n4655579/conf2.mol2> > > > > -- > View this message in context: > http://forums.openbabel.org/OBAlign-error-tp4655579.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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
