Dear all, The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a .cif file to .smi and subsequent generation of coordinates from the .smi file results in the addition of an extra H to one of the ring C atoms. The original cif formula is C7H8N2O4 but this changes to C7H9N2O4, which is no longer a zwitterion.
I also noticed that converting an ion to smi and then from smi to xyz resulted in the addition of hydrogen atoms. Can this be avoided? Is the smi conversion of ions and zwitterions known to cause problems? Many thanks, Scott -- View this message in context: http://forums.openbabel.org/Smiles-conversion-problems-with-Ion-and-Zwitterion-tp4655721.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Keep yourself connected to Go Parallel: TUNE You got it built. Now make it sing. Tune shows you how. http://goparallel.sourceforge.net _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
