questions on this (like all questions) should go to mailing list; I have never looked at how gen3D is implemented or the minimizer that presumably is giving this error, so I am of no help.
-David > On Apr 2, 2015, at 10:25 PM, Matthew Guberman <mat...@optonline.net> wrote: > > Thanks David for your help. I, however, get an error message (below) when > I add the --gen3D keyword. > > WARNING: too small "scale" at Newton2NumLineSearch > > What does this mean? How can I avoid it? > > > >> 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 >> >> >> ----- >> No virus found in this message. >> Checked by AVG - www.avg.com >> Version: 2013.0.3495 / Virus Database: 4311/9437 - Release Date: 04/02/15 >> >> >> > ------------------------------------------------------------------------------ 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
