Example 1

The example directory demonstrates how to run a complete binding free energy calculation with PCC-FECalc. It contains sample settings files and a submission script:

  • pcc_submit_example.py – orchestrates a full calculation using the library classes.
  • ACT_settings.JSON and FEN_settings.JSON – example target molecule configurations.
  • system_settings.JSON – describes simulation parameters and paths used by the submission script.
  • ACT.pdb and FEN.pdb – coordinate files for the acetaminophen and fentanyl targets.

To try the example, adjust the paths in system_settings.JSON as needed and run:

python pcc_submit_example.py

The script will build the PCC, prepare the target molecule, run the enhanced sampling calculation, and post-process the results to report the binding free energy.