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.

	Hydrogen HCl
	Helium He
	Lithium LiCl
	Beryllium Be
	Boron B
	Carbon C
	Nitrogen N
	Oxygen O
	Fluorine F
	Neon Ne
	Sodium NaCl
	Magnesium Mg
	Aluminum Al
	Silicon Si
	Phosphorus P
	Sulfur S
	Chlorine Cl
	Argon Ar
	Potassium KCl
	Calcium ClCaCl
	Scandium Cl[Sc](Cl)Cl
	Titanium Cl[Ti](Cl)(Cl)Cl
	Zinc ClZnCl
	Gallium Ga
	Germanium Ge
	Arsenic As
	Selenium Se
	Bromine Br
	Krypton Kr
	Rubidium [Rb]Cl
	Strontium Cl[Sr]Cl
	Yttrium Cl[Y](Cl)Cl
	Zirconium Cl[Zr](Cl)(Cl)Cl
	Palladium Pd
	Cadmium Cl[Cd]Cl
	Indium [In]
	Tin [Sn]
	Antimony [Sb]
	Tellurium [Te]
	Iodine I
	Xenon Xe
	Cesium [Cs]Cl
	Barium Cl[Ba]Cl
	Lanthanum Cl[La](Cl)Cl
	Hafnium Cl[Hf](Cl)(Cl)Cl
	Mercury Cl[Hg]
	Thallium Tl
	Lead [Pb]
	Bismuth [Bi]
	Polonium [Po]
	Astatine [At]
	Radon [Rn]

view raw elements.smiles hosted with ❤ by GitHub

	import subprocess,sys
	filename = sys.argv[1]
	file = open(filename, "r+")
	for line in file:
	words = line.split()
	name = words[0]
	smiles = words[1]
	smiles = smiles.replace("#","%23")
	smiles = smiles.replace("[","%5B")
	smiles = smiles.replace("]","%5D")
	sdffile = name+".sdf"
	url="https://cactus.nci.nih.gov/chemical/structure/"+smiles+"/sdf"
	subprocess.call(['curl',url, '-o',sdffile])

view raw smiles2coord.py hosted with ❤ by GitHub

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