############### # R E A D M E # ############### This repository contains a minimal dataset of input files required to reproduce the simulation results presented in the paper "The trimeric major capsid protein of Mavirus is stabilized by its interlocked N-termini enabling core flexibility for capsid assembly" by Christiansen et al., 2021, JMB. All simulations were performed using the MD engine GROMACS 5. MD simulations in GROMACS require a coordinate file of the system (.gro), a topology file of the system (.top), and a molecular dynamics parameter file (.mdp). A simulation can be run with the following commands: gmx grompp -c coord.gro -p topol.top -f run.mdp -o run.tpr gmx mdrun -deffnm run Two different types of simulations were performed. ------------------------------------------------------------------------------------- - Structure-based MD simulations of trimeric capsomer (see directory capsomer_SBM/) - ------------------------------------------------------------------------------------- The SBM was built from the capsomer .pdb structure 6g45.pdb. All runs used the same topology file 6g45.top. 6g45.ndx is the system's index file required to analyze the clasp distances as described in the paper. .mdp files can be found in the respective subfolders. Capsomer simulations at constant temperature, starting from native state 6g45.gro: see directory capsomer_SBM/T_const/ Capsomer simulation with simulated annealing, starting from structure with loose N-terminal arms initLoose.gro: see directory capsomer_SBM/SA/initLoose/ Capsomer simulation with simulated annealing, starting from energy-minimized fully dissociated structure em.gro: see directory capsomer_SBM/SA/initDiss/ ------------------------------------------------------------------------------ - Explicit-solvent MD simulations of MCP monomer (see directory monomer_MD/) - ------------------------------------------------------------------------------ All runs initiated from the MCP monomer structure 6g45_single.pdb (extracted as first chain of trimeric capsomer 6g45.pdb). As described in the paper, the structure was energy-minimzed (em.mdp) and neutralized (ions.mdp). Subsequently, the position-restrained structure was NVT- and NPT-equilibrated at each considered temperature (see directories T3??/ for respective .mdp and .gro files). To reproduce the actual MD simulations with GROMACS 5, execute the following commands: gmx grompp -f runT??.mdp -c npt.gro -t npt.cpt -p topol.top -o run gmx mdrun -v -deffnm run Monomer simulation at T = 300 K: see directory monomer_MD/T300/ Monomer simulation at T = 314 K: see directory monomer_MD/T314/ Monomer simulation at T = 325 K: see directory monomer_MD/T325/ Monomer simulation at T = 335 K: see directory monomer_MD/T335/