MD simulation data: Intrinsic disorder is a conserved feature of hepatitis C virus E2 glycoprotein

<strong>Background</strong> Equilibration, relaxation and production runs were performed on GPUs using the CUDA version of PMEMD in AMBER 16 and AMBER ff14SB force field. Minimisation steps were performed on a CPU using PMEMD in AMBER 16 and the AMBER ff14SB force field. The GLYCAM_06j-1 force field was used for the simulations of the glycosylated E2. All software is available from http://ambermd.org/. <strong>Contents</strong> There are three tarball (<strong>.tar.gz</strong>) files, one for each of the HCV strain investigated. The contents of each tarball is as follows: 1. a source PDB (<strong>.pdb</strong>) file 2. <strong>leap.scr</strong> - a script used to create the .prmtop and .inpcrd files 3. Two AMBER parameter/topology (<strong>.prmtop</strong>) (one with hydrogen mass repartitioning) and an AMBER coordinate (<strong>.inpcrd</strong>) file 4. Multiple control (<strong>.ctl</strong>) files numbered 1 to 10 that are used to minimize (<strong>min</strong> prefix), relax (<strong>rel</strong> prefix) and equilibrate (<strong>equ</strong> prefix) the model 5. Executable <strong>do_md</strong> that performed all the minimisation, relaxation and equilibration steps 6. File <strong>parmed.txt</strong> used to repartition the hydrogen atom mass (for the unglycosylated simulations) 7. control file <strong>prod.ctl</strong> used for the production run 8. Executable <strong>run_prod</strong> that was used to perform the production run 9. Two control files (<strong>prod_short.ctl </strong>and <strong>prod_short_2.ctl</strong>) for the short runs used to de-correlate the simulation for the independent runs 10. Executable <strong>run_short</strong> and <strong>run_short_2</strong> used to carry out the de-correlated production runs. 10. Five AMBER trajectory (<strong>.nc</strong>) files for five independent MD simulations, numbered 1 to 5. <strong>Note: </strong>each of these files is over 2GB.