LAT1-metainference

This git contains scripts and files relating to analysis of metainference molecular dynamics(MD) simulations performed on recently published outward-occluded LAT1 cryo-EM structure. (PDB: 7DSL).

For detailed gude on how to set-up metainference simulations, GROMACS topology and input files as well as PLUMED input files, please visit: https://www.plumed-nest.org/eggs/22/018/

The scripts perform 4 tasks:

1. Assembling and concatenate ensemble simulation

   Scripts: assemble_ensemble_xtc.sh

2. Calculation of the RMSD matrix

   Scripts: rmsd_matrix_generation.sh, kkh_get_rmsd_matrix.py

3. Clustering with gromos algorithm

   Scripts: gromos_clustering.sh, gromos_clustering.cpp

4. Analyzing Ensemble Trajectory

   Scripts: 7dsl_traj_analysis.py, gen_interaction_map.py

Dependencies

Gromacs 2020.1

MDAnalysis 2.0

ProLif 3.2

Python 3.6+

RDKit (2020.03+)

Pandas (1.0+)

NumPy

SciPy

tqdm

• Highly recommended to install MDAnalysis and ProLif in an anaconda environment. See the install instructions for those programs.