NPC1L1 MD Simulations

Repository containing files and scripts for molecular dynamics simulations of the transmembrane protein NPC1L1.

The MD simulations were run with Amber (pmemd.CUDA engine), trajectories were preprocessed with cpptraj, analyses were mainly performed with MDAnalysis.

The repository is structured as follows:

• input_structures:
  • 6v3f: Contains the input structures for the NPC1L1 open conformation (PDB ID: 6V3F).
  • 6v3h: Contains the input structures for the NPC1L1 closed conformation (PDB ID: 6V3H).
• scripts-md:
  • set-up-simulations: Contains the scripts and protocols to prepare the files for running the simulations.
  • process-trajectories: scripts for preprocessing the trajectories (requires cpptraj).
• amber_md_config_files: Contains the amber md configuration files.
• scripts-analysis: Contains the scripts for analyzing the simulations.

To build the membrane and topology files:

• scripts-md/set-up-simulations/0-build-membrane-and-top-files.sh.

To run the energy minimization + MD simulation:

• 1-run-energy-min.sh
• 2-run-md.sh

To run the analysis:

• scripts-analysis/...

The results are stored in the final_data directory.

The figures/plots are stored in the final_plots directory.