md-analyzer

A simple python script to facilitate the analysis of the MD trajectory of protein-ligand complexes produced by OpenMM and Gromacs.

Introduction:

This python script provides a simple way to perform the routine analysis of MD trajectory of protein or protein-ligand complexes generated by OpenMM and Gromacs. The periodic boundary conditions (PBC) will be corrected before the analysis were performed, and 5 functions were provided as followed:

(1) rmsd: Calculate the RMSD of protein heavy atoms, backbone, Cα, and ligand of the MD trajectory. The result will be saved as a png file and a csv file containing the corresponding row data. (2) extract complex: Extract frames from the MD trajectory within the specified time range and save them as a PDB file. (3) distance analysis: Calculate the distance changes between two atoms, indicated by atom label, in the MD trajectory. The result will be saved as a png file and a csv file containing the corresponding row data. (4) ligand rmsf: Calculate the RMSF of the ligand in a MD simulation. The result will be saved as a png file and a csv file containing the corresponding row data. (5) protein-ligand fingerprint: Calculate the interaction of between the protein and ligand in the MD trajectory.

Installation:

The following installation is built on the previous installation, with one additional package, ProLif, required for the calculation of protein-ligand fingerprint. Please use the following command:

# create a new virtual environment:
conda create -n mdanalyzer python=3.9
# activate virtual environment
conda activate mdanalyzer
#install mdanalysis 
conda install -c conda-forge mdanalysis
# install prolif
conda install -c conda-forge prolif

Usage:

1. Please put this script outside of the folder containing your MD results. For example, the MD topology file and MD trajectory are located at /data/usr/md1, please put this script to /data/usr
2. Go to the directory: cd /data/usr
3. Type: conda activate openmm to activate the virtual environment
4. Type: python md_analyzer.py, and the following message will show: please input the name of working directory:
5. Type the name of the MD folder: md1 and the following message will show: please specify the name of the pdb file and dcd file e.g. com.prmtop, traj.dcd
6. For MD result produced by OpenMM, please use the .prmtop/.pdb and .dcd as: com.prmtop,com.dcd or com.pdb,com.dcd For MD result produced by Gromacs, please use the .gro and .xtc file as: com.gro,com.xtc The following message will show: apo structure? (1) Yes (2) No
7. For a protein-ligand complex, please type 2 and the following message will show after the load of data is finished. Please select the analysis by type 0-5 to perform your analysis.

please select the mode:
(1) rmsd
(2) extract complex
(3) distance analysis
(4) ligand rmsf
(5) protein-ligand fingerprint
(0) quit

8. The results will be saved in the /data/usr/md1/analysis