# FEP
Code to run FEP on a protein-ligand system using Yank. The input files are for the h4w3 system.

## List of files

* **yank_condaenv.yml** contains the conda environment used for FEP calculations with Yank

### Input files:
* **yank.yaml** is the input file for Yank with the options for the FEP calculation
* **system_solvent.pdb** is the system structure for the ligand alone
* **system_solvent.xml** is the openmm simulation input file for the ligand alone
* **system_complex.pdb** is the system structure for the protein-ligand complex
* **system_complex.xml** is the openmm simulation input file for the protein-ligand complex
  
### Run files:
1. **yank.sh** is a slurm job script that runs the FEP calculation using Yank with yank.yaml as the input file
2. **yank_analyze.sh** is a slurm job script that takes the output from yank.sh and calculates the absolute ΔG of binding using MBAR (along with other analyses)
3. **yank_gettraj.sh** is a slurm job that extracts the trajectories as xtc files.
4. **endstate.sh** is a slurm job that runs an extended endstate simulation.
  
### Result files:
* **yank_analysis.pkl** containts the results of the analysis in pickle format