> I am having trouble getting Confab to generate structures based on the > attached structure. I am using the command: … > ..Energy cutoff = 50 > . (snip) > ..below energy threshold = 0
> Any ideas to why Confab is not producing conformers? It’s telling you up-front. Nothing is below the energy cutoff of 50 kcal/mol. I looked briefly at that file, and MMFF was giving me an energy of 900+ kcal/mol. (Hey, it’s a big polymer.) If you change the ecutoff, you’ll be fine: http://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html Not sure what the best cutoff will be, but something like this perhaps: obabel ~/Desktop/polymer.mol2 -O confs.mol2 --confab --conf 10000 --verbose --ecutoff 1500 You can also look at other conformer generation options in Open Babel that ignore energy cutoffs.. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
