> 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 ------------------------------------------------------------------------------ Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
