On Thu, Nov 10, 2016 at 12:34 PM, Tim Potter <thetimpot...@gmail.com> wrote: > Thank you so much for your offer to help. I'm happy to help user document > avogadro when you get to that point. I started trying avogadro 2 because > avogadro 1 was not saving double bonds, and was also not aware that avogadro > 1 had these extension capabilities. I saved the file in CML which solved > both issues - I was able to open the file in avogadro 2 and also the double > bond information that was created in avogadro 1 displayed in avogadro 2.
I am glad this helped, CML saves bonding information whereas PDB has only limited support. > > Great, thank you for offering guidance. I used avogadro 1 to calculate the > energy at [Energy = 9,515.9 kJ/mol]. The wiki does not detail exactly what > is meant by this figure. What is the context for the kJ/mol figure? > I think that is the energy calculated by Open Babel using a molecular mechanics force field. You would need to use an input generator, and run a quantum code if you wanted to get a more accurate number (that would also be slower in general). ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
