Hi all, I am trying to extract the structure from the following strangely formatted mol file:
BASIS cc-pVTZ PP EXCITATION DIAGNOSTIC Atomtypes=3 Nosymmetry Charge=6.0 Atoms=10 C 2.2706222585 4.7730173284 0.0000000000 C -2.2706222585 4.7730173284 0.0000000000 C 0.0000000000 6.1111121474 0.0000000000 C 2.2816826330 2.1387165841 0.0000000000 C -2.2816826330 2.1387165841 0.0000000000 C 0.0000000000 0.7923464742 0.0000000000 C 2.1197819099 -3.4258994126 0.0000000000 C -2.1197819099 -3.4258994126 0.0000000000 C 1.3395610232 -5.9107336961 0.0000000000 C -1.3395610232 -5.9107336961 0.0000000000 Charge=7.0 Atoms=1 N 0.0000000000 -1.8918071168 0.0000000000 Charge=1.0 Atoms=9 H 4.0627785591 5.7776147665 0.0000000000 H -4.0627785591 5.7776147665 0.0000000000 H 0.0000000000 8.1643586785 0.0000000000 H 4.0806204132 1.1593701311 0.0000000000 H -4.0806204132 1.1593701311 0.0000000000 H 4.0065792553 -2.6563688490 0.0000000000 H -4.0065792553 -2.6563688490 0.0000000000 H 2.5755781273 -7.5400732042 0.0000000000 H -2.5755781273 -7.5400732042 0.0000000000 I've tried just using the coordinates but I get an error for setting up the forcefield. The coordinates are taken from MP2 calculations but when I view the structure in avogadro the interatomic distances are all too long. It looks like they need to be scaled. Any advise here? All the best, Scott -- View this message in context: http://forums.openbabel.org/Unable-to-set-up-forcefield-for-coordinates-from-mol-file-tp4656682.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
