Quantum Chemistry for the masses

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Setting it up

Install Phenix

Install gamess

Create a SMILES string for your molecule

SMILES stands for "simplified molecular input line entry specification"

Simple examples:

  • Ethanol: CCO
  • Cyclohexane: C1CCCCC1
  • Benzene: c1ccccc1

For more involved molecules, or to learn the language interactively, try a Java Molecular Editor

Draw the molecule in the JME


Calculate Properties


Copy the SMILES string

eg: O=C(Oc3ccc(c1cc(NS(=O)(=O)O)c(Cl)cc1c2cccc(C(O)(O)O)c2)cc3Br)C4CC4

Run the Calculation as a single unix command


phenix.elbow --games --smiles="O=C(Oc3ccc(c1cc(NS(=O)(=O)O)c(Cl)cc1c2cccc(C(O)(O)O)c2)cc3Br)C4CC4"

or specify method and basis set:

phenix.elbow --games  --basis="3-21G(d,p)" --method=mp2  --smiles="O=C(Oc3ccc(c1cc(NS(=O)(=O)O)c(Cl)cc1c2cccc(C(O)(O)O)c2)cc3Br)C4CC4"

or just use molecular mechanics energy minimization, if you don't need or want a QM treatment (this is much faster):

phenix.elbow --opt --smiles="O=C(Oc3ccc(c1cc(NS(=O)(=O)O)c(Cl)cc1c2cccc(C(O)(O)O)c2)cc3Br)C4CC4"

Note the use of double-quotes to protect the special characters like parentheses.

You will get a series of files, here listed in reverse chronological order:

-rw-r--r--    1 wgscott   wheel        1K Jun  4 20:13 elbow.001.bonding.py
-rw-r--r--    1 wgscott   wheel       14K Jun  4 20:13 elbow.001.cif
-rw-r--r--    1 wgscott   wheel      211K Jun  4 20:13 elbow.001.pickle
-rw-r--r--    1 wgscott   wheel        1K Jun  4 20:13 elbow.001.options.pickle
-rw-r--r--    1 wgscott   wheel        5K Jun  4 20:13 elbow.001.pdb
-rw-r--r--    1 wgscott   wheel        6M Jun  4 20:13 elbow.001.gamess.gam
-rw-r--r--    1 wgscott   wheel       42M Jun  4 20:13 elbow.001.gamess.dat
-rwxr--r--    1 wgscott   wheel      417B Jun  4 20:11 elbow.001.gamess.csh*
-rw-r--r--    1 wgscott   wheel        3K Jun  4 20:11 elbow.001.gamess.inp
-rw-r--r--    1 wgscott   wheel        5K Jun  4 20:11 elbow.001.pre_opt.pdb

The file elbow.001.pdb contains the refined coordinates in pdb format, and elbow.001.gamess.gam in gamess format for viewing in PyMol or ghemical,

View the result


pymol $(ls -t *.pdb | head -n 1 )



ghemical $(ls -t *.gam | head -n 1 )


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