ATM

An experimental Python package to run free energy calculation using AToM-OpenMM

Installation

Step 1 Install Miniconda3
Step 2 Install conda-lock and mamba by:

  conda install -c conda-forge conda-lock
  conda install -c conda-forge mamba

Step 3 Install the ATM package by:

  git clone https://github.com/EricChen521/atm.git
  cd atm
  PYTHONPATH=. python dev/install.py

Step 4 Install UWHAT packagge in the atm-dev env by:

conda activate atm-dev
Rscript -e 'install.packages("UWHAM", repos = "http://cran.us.r-project.org")' 

Step 5 Install AToM-OpenMM by following the insructions from Dr. Emilio Gallicchio's lab here. Do not need to install the virtual env, use the atm-dev env instead.

Step 6 Update the system settings and input file paths such as protien, ligands and cofactor in atm_config.yaml:

atm_pythonpathname
atom_build_pathname
is_slurm
gpu_devices 

Step 7 Activate the env and run the ATM calculation

conda activate atm-dev
atm -c atm_config.yaml

Good luck!