> Is there a way to tell babel what the charge of the molecule in the xyz file > is?
From the command-line? No. Even if there was, it’s not going to suddenly assign formal charges to your de-protonated functional groups. (Yes, as humans we can find the most likely places to put the negative charges, but there’s nothing in the codebase that can do that.) -Geoff ------------------------------------------------------------------------------ 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
