Hi, as far as I know, the current version of OB doesn't handle gracefully stereogenic centers in rings, but I believe the version in the GitHub repo (that's going likely to be the next stable one) should do that.
About protonation states, you could try to use the '-p' option to set the pH you want to simulate. Although, I have to say that the stable version (2.3.2) is known to have problems with that. A solution would be to download the latest code from GitHub and compile it yourself[1], if you know how to do it. S [1] https://openbabel.org/docs/dev/Installation/install.html#compiling-open-babel On 03/08/2016 05:08 AM, mirix wrote: > I am generating 3D structures from canonical SMILES and I am facing several > issues. > > The first is that OpenBabel does not seem to be able to produce structures > with the right sterochemistry in certain cases (even if it is explicitly > indicated in the SMILES). As far as I can tell, this happens with fused > rings where both (contiguous) shared atoms are sterocenters. > > The workaround I found is converting the SMILES to mol2 with Balloon > (because Omega2 fails with a few of them) and then: > > obabel ${ligandid}.mol2 -O ${ligandid}.sdf --conformer --nconf 200 --score > energy --writeconformers > > The problem is that obabel seems to reprotonate certain functional groups > (such as carboxylic acids which are deprotonated on purpose). Is there a way > to prevent such behaviour? > > > > > -- > View this message in context: > http://forums.openbabel.org/Is-there-a-way-to-prevent-re-protonation-during-conformer-generation-tp4659206.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Stefano Forli, PhD Assistant Professor of Integrative Structural and Computational Biology, Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112A The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
