/host-torsions

host-torsions repo

Primary LanguageJupyter Notebook

What's here

Repo for the host-torsions project.

OpenFF came out with Bespokefit which builds custom torsion parameters for individual molecules. This will be used to build custom torsions for several host systems. Afterwards, free energy calculations will be run to see what difference the customs torsions make, and how these impact host-guest binding predictions.

Conformer and charge generation is tricky for larger macrocycles, so bespoke cannot be run on the entire host. Instead, each host that gets looked at will be chopped up into its repeating units, then run through bespoke. Afterwards, the parameters will be applied to the entire host system.

Host to do list:

Setting up Bespokefit for this project:

  1. Clone OpenFF Bespokefit repo
  2. Add xtb-python to bespoke-fit/devtools/conda-envs/test-env.yaml
  3. Create environemnt from testing environment conda env update -n bespoke --file bespoke-fit/devtools/conda-envs/test-env.yaml. Install additonal packages: conda install -c conda-forge mamba seaborn.
  4. Execute python setup.py develop in bespoke-fit/
  5. Run pip install git+git://github.com/openforcefield/bespoke-fit.git@931bb66bb3700208616e41bfde1a80d90a37d74f to get desired environment.
  6. Openeye fragmenter issue workaround: git clone https://github.com/openforcefield/openff-fragmenter.git | cd and git checkout continue-if-elf-fails | execute python setup.py develop
  7. Env saved to env.yml

📂 Directory

  • run.py - script to run bespokefit on input molecule. Takes a SMILES string and ID. Creates a folder with results based on the input ID. Command: python run.py -smiles 'BrCO' -id BrCO
  • run_all.py - Script to run run.py on a CSV containing multiple SMILES. Command: python run_all.py -fragments_csv_file host-systems/fragments.csv
  • How_to_train_your_forcefield.ipynb - Notebook taken from OpenFF blogpost on how to use Bespokefit.
  • host-systems/ - Contains original host files and, fragments of the host, images of the fragments, and a .csv file that contains fragment ID's and SMILES strings.
  • OA-fragment-*/ - Bespokefit results for a specific host fragment.