Hi,
On Sun, May 30, 2010 at 6:11 PM, bouille <ambin...@wanadoo.fr> wrote: > > Using the script below from Marschall > > I got the following error > > CC[C@@H]1COP23OC[C@@H](CC)N2CCN13 |r| > Traceback (most recent call last): > File "/home/bouille/DescriptorsCalcul/test3D.py", line 59, in <module> > if optimizesubroutine(molH)==0: > File "/home/bouille/DescriptorsCalcul/test3D.py", line 25, in > optimizesubroutine > optimizeresult = AllChem.UFFOptimizeMolecule(mol,1000) > RuntimeError: Invariant Violation > > Thank you for your help It looks like this is a bug in the way the force field is built for 5-coordinate atoms. I've added a bug report for it: https://sourceforge.net/tracker/?func=detail&aid=3009337&group_id=160139&atid=814650 and will get it fixed for the next release. Thanks for reporting the problem, -greg ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
