Residue orientation analysis for substrate's residue side chains when translocating through TIM.
- python >= 3.10.10
- MDAnalysis >= 2.2.0
- numpy >= 1.24.2
- matplotlib >= 3.7.1
The above dependencies can be installed using Anaconda or any other package manager.
Run the analysis script pub_analyze_residues_orientation.ipynb in Jupyter Notebook.
- Structure and run input files:
.gro,.tpr - SMD trajectories:
.xtc
Running the analysis script will generate a figure illustrating residue orientation distributions. The process typically completes within a few minutes.