Source code for the paper: Molecular basis and function of scramblase VMP1 in complex with lipid transfer protein ATG2A

This repository contains input files and analysis code used in the paper.

Contents

1) Simulations

The Simulation/ folder contains the input files required to run atomistic simulations with GROMACS 2022.5

Simulation trajectories are not included in this repository. For questions about accessing or using the trajectories, please contact:

• yc638@cam.ac.uk
• yongwang_isb@zju.edu.cn

2) Trajectory analysis

Trajectory_analysis.ipynb contains the analysis workflows used in the paper, including:

• POPC/water density analysis
• Protein–protein and protein–lipid (POPE) contact analysis
• Scrambled-lipid identification and counting
• Cavity volume approximation
• Tilt angle calculation

Some analyses require external tools:

• GetContacts
• Scramblyzer
• PLUMED