Conformational search

autoENRICH can run conformational searches using RDKit.

  1. To run a conformational search start with the following command from inside your autoenrich molecule folder:
    > autoenrich molecule_name conf_search
    

    This will create a conf_search folder, containing a python script to perform the conformational search using RDKit. A submission script will also be created, depending on the submission system you are using.

  2. Run the conformational search (or submit it to a queue on HPC)
    > bash confsearch_molecule_name.sh # To run locally
    > qsub confsearch_molecule_name.sh # To submit on a PBS system
    > sbatch confsearch_molecule_name.sh # To submit on a SLURM system
    

    This will perform the conformational search using RDKit to find conformers for your molecule, then it will remove conformers based on energy or similarity to provide the number of conformers specified in the preferences file.

Your autoenrich folder should look like this:

- my_autoenrich_folder/
	- molecule_name/
		- molecule.xyz
    - molecule.pkl
    - molecule_nameBACKUP.pkl
    - ENRICH.json
    - confsearch_molecule_name_.sh
    - conf_search/
      - do_confsearch.py

The next step is to set up DFT geometry optimisations for the conformers produced in this step.