On 30/11/2012 12:03, scott_m wrote: > 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?
Getting added hydrogens right is a recurrent issue. However the conversion from SMILES to xyz (and other formats) seems ok. Your problem may be in the conversion of the cif file, but you will need to append it for somebody (probably not me) to debug. obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz --gen3D --title "" --append formula 21 C7H8N2O4 C 2.45602 0.70570 1.56344 O 3.44592 0.48586 2.25208 O 1.43656 1.46670 2.00415 C 2.26356 0.11437 0.19030 C 3.14546 0.74947 -0.88078 H 2.84831 0.31396 -1.84634 C 2.83038 2.27406 -0.99631 O 1.67090 2.60592 -0.61087 O 3.79441 2.97728 -1.40748 N 4.60137 0.42805 -0.71225 C 5.35900 0.94762 0.25841 N 6.58789 0.46124 0.10334 H 7.33992 0.61660 0.75954 C 6.69161 -0.15933 -1.12882 C 5.43119 -0.14873 -1.66026 H 0.84536 1.76580 1.27272 H 1.20439 0.19509 -0.08254 H 2.46795 -0.95767 0.27113 H 5.04774 1.61643 1.05753 H 7.65241 -0.48371 -1.46628 H 5.01646 -0.45579 -2.60586 1 molecule converted Chris ------------------------------------------------------------------------------ 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
