Molecular-dynamics-Interaction-plot

Two scripts for MD interaction analysis (similar to interaction fraction on Desmond).

How to use:

1. Set your pdb_file_name and ligand_code (UNL, UNK, LIG, etc.) on the "run_interact.sh".
2. Run "run_interact.sh" where your pdb file is located.
3. Run "run_interact.py" in the same directory.

How the script works:

• The analysis is based on a *.pdb file that contains "n" number of frames from a MD.
• The frames are split into individual *.pdb files.
• PLIP analysis is performed to determine the type of interactions for each frame.
• The molecular interactions are sorted in different files .
• Data is concatenated and sorted for appropriate plotting.

Requirements:

• PLIP software.
• Python modules: os, Numpy, Pandas, CSV, matplotlib, pylab.

Bonus:

• A tcl-script (get_pdb_frames.tcl) to get frames from MD trajectories using VMD.

Important: The code is freely distributed without any warranty.