Ralf Bartenschlager2025-04-292023-11-132023-11-13https://datakatalogi.helsinki.fi/handle/123456789/4637The molecular dynamics (MD) simulation dataset. The contents: 5ire_BIOMT_expanded.pdb: The complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE)  5ire_Mprotein_BIOMT_expanded.pdb: The M proteins extracted from the complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE).  The biological assembly shows the dimeric organization of M proteins. 0chol.zip, 10chol.zip, 20chol.zip, and 30chol.zip contain simulation input and output files for the simulated membrane compositions: 0:100, 10:90, 20:80, 30:70 (mol%:mol%) Cholesterol:POPC, respectively.  In each zip file, there are 5 directories: wt, R253L+F257A, R253L+F257S, K275L+Y278A, K275L+Y278S corresponding to each simulated M protein dimer variant: wild type, CARC 2-A, CARC 2-S, CARC 3-A, and CARC 3-S. In each directory, there are the following files: toppar: This directory contains all force field topologies and parameters topol.top: GROMACS topology (top) file index.ndx: GROMACS index (ndx) file prod.mdp: GROMACS MD parameters (mdp)  file 0, 1, 2, 3, 4, 5, 6, 7, 8, 9: These directories contain the simulation inputs and outputs for each simulation repeat. In each of these directories, there are the following files:  t0.pdb: The pdb file of the starting coordinates prod0.tpr: GROMACS binary run input (tpr) file  prod0.edr: GROMACS energy (edr) file prod0.gro: GROMACS output coordinates and velocities after 1 microsecond of simulation prod0.cpt: GROMACS checkpoint file after 1 microsecond of simulation noW.pdb: The pdb file of the starting coordinates with all water molecules removed noW.xtc:  GROMACS compressed trajectory (xtc) file with all water molecules removeddataset