You didn’t tell open babel to generate coordinates. It appears to did tell it to add hydrogens
Telling it to generate 3D coordinates: $ obabel -:'[S@]1(C)[Au][S@]([Au][S@](C)[Au][S@]([Au]1)C)C' -oxyz -h --gen3D 24 S -2.62740 -0.17895 0.14170 C -2.95652 -0.06942 1.92286 Au -2.24638 -2.06745 -1.14324 S -0.11818 -2.09861 -0.28261 Au 1.89511 -2.17472 0.80676 S 2.20125 0.12863 0.66093 C 3.92224 0.01448 1.18651 Au 1.83968 2.31605 -0.06418 S -0.44089 2.12806 -0.40033 Au -2.71597 1.96368 -0.68434 C -0.23724 1.65264 -2.14473 C 0.66688 -1.60577 -1.85429 H -2.50240 -0.94022 2.43830 H -4.05013 -0.02891 2.09256 H -2.44081 0.81997 2.34645 H 4.39348 -0.87682 0.71890 H 3.96471 0.00107 2.29161 H 4.46701 0.88989 0.77694 H 0.83780 1.49732 -2.37109 H -0.61354 2.43632 -2.82909 H -0.76613 0.69183 -2.30679 H -0.09093 -1.58978 -2.66501 H 1.47350 -2.29492 -2.17906 H 1.06196 -0.59053 -1.73039 > On Apr 2, 2015, at 1:16 PM, Matthew Guberman <mat...@optonline.net> wrote: > > Hello, > > I need to convert a SMILES string (below) to xyz coordinates. When > I try to do this, the correct structure is shown in Firefox, but the > list of coordinates (below) contains only zeros, and when I save the > output as a PDB (so I can view it in Chimera), I only see a single Au > atom. How can I fix this problem? > > SMILES string: > [S@]1(C)[Au][S@]([Au][S@](C)[Au][S@]([Au]1)C)C > C:\Users\MGP\Desktop\au4-4me.log > > xyz output > > 24 > > S 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > Au 0.00000 0.00000 0.00000 > S 0.00000 0.00000 0.00000 > Au 0.00000 0.00000 0.00000 > S 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > Au 0.00000 0.00000 0.00000 > S 0.00000 0.00000 0.00000 > Au 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > H 0.00000 0.00000 0.00000 > > > > Thanks, > Matthew > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
