Dear Tayeb, Apologies - it seems like your e-mail to the list “fell through the cracks."
> when dealing with alcohols, amines, carboxylic acids, or other molecules > having dihedrals involving atoms that only have hydrogens and one > substituent. This means the exhaustive conformer search does not actually > examine all the conformers for these cases. In general, hydrogen atoms are ignored in conformer searches because they can rapidly thermalize experimentally and it’s hard to pin them down on XRD experiments. So no, there’s no “missing option” as far as searching hydrogen dihedrals. That said, if you want to edit this, you can change the code: https://github.com/openbabel/openbabel/blob/master/src/bond.cpp#L180 That conditional can be changed to take a look at O-H or N-H, etc. bonds in a dihedral. Hope that helps, -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
