Two scripts for MD interaction analysis (similar to interaction fraction on Desmond).
How to use:
- Set your pdb_file_name and ligand_code (UNL, UNK, LIG, etc.) on the "run_interact.sh".
- Run "run_interact.sh" where your pdb file is located.
- 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.
