Alchemistry with betalactamases

This repository contains the input data for the AFE and MD workflows that can be input to the meze workflow

The scripts folder is split into md and afe:

• md: The slurm_md.sh script can be used to run MD with the meze workflow for all ligands, or using the script 10_md.sh directly. The file paths should be changed as needed in these two scripts. There is also an example cpptraj.in file that can be used to calculate the RMSD of the active site + ligand of the metal protein.
• afe: Similar to the MD workflow, the slurm_all.sh can be used to run the whole workflow, or each of the scripts for solvation, equilibration, etc. can be ran separately as needed.

The MD workflow has a similar directory hierarchy as meze:

/path/to/project/
    |--- inputs/                Input files (set-up by user)
    |   |--- ligands/           Ligand .sdf or .mol2 files (set-up by user)
    |   |--- protein/           Protein .pdb file (set-up by user)
    |--- outputs/               Folder for saving the results of MD runs
    |--- md_input_files/        Input files for running the MD runs
    |   |--- protocol.dat       Datafile with network information
    |   |--- ligands.dat        Datafile containing ligand names, e.g. ligand_1, ligand_2, ...
    |   |--- 10_md.sh           Bash script to run an individual MD simulation with AmberMD.
    |   |--- slurm_md.sh        SLURM script which executes all of the above bash scripts
    |--- equilibration/         Folder for saving the minimisation and equilibration outputs for bound ligands
    |--- logs/                  Folder for keeping SLURM log files

Note that this part of the meze code is still under development, so the MD input files will have to be set up manually.