Now thin wrapper of psi4 named psikit can generate cube file which has frontier orbital information. After calling getMOview, I would like to check the orbital shape.
Psi4 provides vmd_cube.py script which generates cool view on VMD. To run the script on python3, it is needed to change line 332 from ‘for k,v in options.iteritems():’ to ‘for k,v in options.items():’.
After changed the code. Ready to visualize molecular orbital! Let’s check it.
I run the following code on jupyter notebook.
import os import sys import pandas as pd import numpy as np from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole sys.path.append('/Users/iwatobipen/develop/chemoenv/psikit/psikit/') from psikit import Psikit pk = Psikit() pk.read_from_smiles('COc1ccncc1') pk.optimize() >Optimizer: Optimization complete! >-360.5913889506649
Then call getMOview() to generate MO cube files.
Next, run the vmd_cube.py. The script has many options. To check the option, vmd_cube.py -h gives help.
I run the code interactive mode. After run the code, I could see MO on VMD.
To run the code, reader need install VMD in your PC. Of course the script generates image of each MO.
I think it is interesting that visualize MO of protein-ligand complex because it will show interaction of protein and ligand. It is very useful for understanding of the interaction. Any comments or suggestions are greatly appreciated. ;)