On 2013-11-08 04:05, Igor Leontyev wrote: > Dear Geoffrey, > Thanks for your response. > The structure was optimized at MP2/aTZ level. I use XYZ-format because it > is the main format in MolPro QM program. The problem with C=N bond was met > in several compounds listed bellow. Is aTZ an abbreviation for aug-cc-pVTZ? In that case you should get decent results with an optimization like that.
However even for good geometries OB has problems with bond orders sometimes as I pointed out the other day. Is there anything that can be done about that? Changing smiles? > Methanimine > EthanImine > VinylImine > Benzenemethanimine > and Imidazoline > > The definition of sp2 nitrogen via just angle seems to be little > oversimplified. There are cases when angles are significantly distorted, > especially in ring compounds. See for example, the C-N-CH2 angle in > Imidazoline is only 103. > > 11 > Imidazoline.xyz > C -0.88262 -0.68699 0.03537 > N -0.92913 0.64788 -0.34690 > C 0.38783 1.18838 0.01773 > C 1.22818 -0.09818 -0.01329 > N 0.27522 -1.19770 0.25046 > H -1.80129 -1.25731 0.09109 > H -1.74753 1.17193 -0.07458 > H 0.36896 1.62120 1.02219 > H 0.72296 1.93780 -0.69462 > H 2.03179 -0.10284 0.71867 > H 1.66075 -0.25683 -1.00408 > > Thank you though for pointing the reason. > Igor > >>> I came across a problem of converting XYZ to HIN format for imine >>> compounds. In more detail, the double C=N bond in imine series is >>> determined as a single bond. (As a result, atom typification for Merck >>> force field is completely screwed up.) >> >> The problem here is that the H-N-C bond angle is 110 degrees. It's not >> anywhere close to "looking like" an sp2 nitrogen. So the PerceiveBondOrders >> is left assuming there's some missing valence somewhere. >> >> It might be worth having some sort of special case for indicating that "all >> hydrogens are included, so funny angles are OK" but I'm a little hesitant >> because this doesn't come up very often. >> >> Out of curiosity, where did this file come from? Some calculation? Why did >> you use XYZ? I'm wondering why the angle is so off and whether a different >> format would preserve the bond information for you. >> >> If others have bad experiences with imines, I'd like to know. >> >> Thanks, >> -Geoff >> >> > > ------------------------------------------------------------------------------ > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
