User Guide

Prerequisites

• For installing the scripts, Miniconda or Anaconda is required.

Step 1. Set up running environment

1.1 Download the source code and create the conda environment

git clone https://github.com/reuter-group/MD-contacts-analysis.git
cd /path/to/MD-contacts-analysis
conda create -f md-ana-py37.yml

1.2 Activate the environment

conda activate md-ana-py37

Step 2. Prepare a config file

The config file sets parameters for the analysis; check detailed explanation of each parameter. An example config file config_example.json:

{
    "PSF_FILE": "test_data/reza_data.psf",

    "DCD_FILE": [
        "test_data/reza_data_64frames.dcd"
    ],

    "RESIDUE_FILE": "test_data/reza_data_short_candidates.txt",

    "hbond_lipids": ["POPC", "POPE", "POPI", "POPS", "CHL1", "PSM", "SAPI24"],
    "hydrophobic_lipids": ["POPC", "POPE", "CHL1", "PSM", "SAPI24"],
    "cation_pi_lipids": ["POPC", "POPE", "POPS", "SAPI24", "PSM"],    

    "lifetime": 2, 
    
    "mem_limit": 4,

    "start": 0,
    "stop": null, 
    "step": 1,

    "output_file_prefix": "test-reza"
}

Step 3. Run analysis script

Choose from one of the following scripts to run:

• Hydrogen bonds: hbond_ana.py
• Hydrophobic contacts: hydrophobic_ana.py
• Cation-Pi interactions: cation_pi_ana.py

(md-ana-py37) $ ./<analysis_code>  <configuration_file>

## for example, run hbond analysis
(md-ana-py37) $ ./hbond_ana.py config_example.json