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.



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