## Saturday, November 5, 2016

### Generating coordinates for molecules with diverse set of elements

It looks like PM6 in GAMESS is working, but we need to test it for more elements.  Here's how I generated the MOPAC input files.  First I made a list of SMILES strings for for most of the elements, which I then converted to sdf files with smiles2coord.py.  The I used OpenBabel to convert to MOPAC input files.

The implementation is only done for RHF so the molecules need to be closed shell.  So, for example for Sc I used ScCl$_3$ For many of transition metals I couldn't really think of a closed shell molecule, so I didn't include those elements.  For the non-metals the Cactus server automatically adds hydrogen.  Cactus also interprets names like Sc as sulphur, so square brackets are needed.