Dear OB users, 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.)
See the output hin-file bellow, the C=N bond order is determined as "s"-single while it should be "d"-double. Any idea why the problem arises? Thank you. Command line: "obabel -ixyz Methanimine.xyz -ohin" Input structure: Methanimine.xyz 5 Methanimine.hin C 0.01809 -0.61489 0.00000 N 0.09201 0.65950 0.00000 H 0.94072 -1.18704 0.00000 H -0.91505 -1.17842 0.00000 H -0.84531 1.06292 0.00000 Output structure: mol 1 "Methanimine.hin" atom 1 - C ** - 0.02453 0.01809 -0.61489 0.00000 3 2 s 3 s 4 s atom 2 - N ** - -0.25531 0.09201 0.65950 0.00000 2 1 s 5 s atom 3 - H ** - 0.04510 0.94072 -1.18704 0.00000 1 1 s atom 4 - H ** - 0.04510 -0.91505 -1.17842 0.00000 1 1 s atom 5 - H ** - 0.14058 -0.84531 1.06292 0.00000 1 2 s endmol 1 Expected output: mol 1 charge 0 atom 1 - C C= - +0.000 +0.01808907 -0.61489025 +0.00 3 2 d 3 s 4 s atom 2 - N N= - +0.000 +0.09201153 +0.65949762 +0.00 2 1 d 5 s atom 3 - H HC= - +0.000 +0.94072289 -1.18704357 +0.00 1 1 s atom 4 - H HC= - +0.000 -0.91505199 -1.17841970 +0.00 1 1 s atom 5 - H HN= - +0.000 -0.84531475 +1.06292463 +0.00 1 2 s endmol 1 ------------------------------------------------------------------------------ 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
