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How to submit a geometry optimization job of Emim using Gaussion

Build Status

Create the SMILES of Emim

  1. Draw a structuer of Emim in ChemDraw.
  2. Select the whole structure, right click, then go to "Molecule --> Copy as --> SMILES" and click. image
  3. Now the SMILES of your selected structure will be copied to your clipboard.

Convert the SMILES of Emim to 3D structure and optimize the 3D structure based on force field using python

  1. Import the python modules which will be used in the next steps. Type the fllowing code in your jupyter notebook and run.
from rdkit import Chem
from rdkit.Chem import AllChem
  1. Read the SMILES string using Chem.MolFromSmiles, and write it into a variable named "mol". Use the fllowing code.
mol = Chem.MolFromSmiles('CN1C=[N+](CC)C=C1')
mol

image

  1. Add hydrogen atoms to "mol".
mol = Chem.AddHs(mol)
mol

image

  1. Convert "mol" to 3D structure and optimize the 3D structure using a universial force field.
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
mol

image

  1. Convert "mol" to xyz format and print.
xyz = Chem.MolToXYZBlock(mol)
print(xyz)

image

These coordinates of the force field optimized 3D structure will be used in the next steps.

Make a Gaussion input file and submit the optimization job in the cluster

  1. Make a new text file in your computer. Then copy the following to the new text file.
%mem=3200MB
%nproc=8
% chk=Emim.chk
# B3LYP/6-311+G(d, p) opt freq

Emim

1 1

image

  1. Copy the corrdinates of the optimized 3D structure generated before to this text file. Please note that copy the corrdinates part only.

image image

  1. Connect to the cpu cluster and make an input file.
  • Connect to the cpu cluster using your terminal
  • make a new folder named run_Emim_opt using the flowing command line
mkdir run_Emim_opt
  • enter the new folder using the following command line
cd run_Emim_opt
  • make a new file named Emim_opt.com and edit it using vim
vi Emim_opt.com

image

  • copy the content in the new text file made previously image

  • go back to the terminal connected to cpu cluster

  • type i to go to the insert mode of vim image

  • paste the copied content image image

  • type Esc to exit from the insert mode image

  • type:wq to save the file and quit from vim and press enter image

Submit the optimization job

To submit the job using the fllowing command

g16 Emim_opt.com