Computational analysis of the dynamics and energetics of the HIV-1 MA lattice in complex with a lipid bilayer of authentic HIV-1 lipidome composition

This repository contains the necessary inputs and scripts to run and analyze the molecular dynamics simulations of the HIV-1 MA protein lattice in its immature and mature arrangements in complex with a lipid bilayer with composition resembling the HIV-1 membrane lipidome. The simulations are described in Chen, L., Hikichi, Y., Rey, J. S., Akil, C., Zhu, Y., Veler, H., ... & Zhang, P. (2024). Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity. bioRxiv.

The inputs and scripts are divided in one directory for the immature MA lattice analysis and one for the mature MA lattice. Each directory contains subdirectories with the scripts necessary to set up preparation and production MD simulations of each system as well as an analysis/ folder with useful scripts for analyzing the simulation trajectories. Requirements:

• MD simulations: NAMD 3
• Trajectory analysis: VMD, python3, GROMACS (for gmx filter)
• MMPBSA interaction energy calculations: Amber

PDB and PSF files can be found in the Zenodo repository https://doi.org/10.5281/zenodo.14994451