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

<p><strong>Background</strong></p> <p>Equilibration, relaxation and production runs were performed on GPUs using the CUDA version of PMEMD in AMBER 16 and AMBER ff14SB force field.&nbsp;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.&nbsp;All software is available from http://ambermd.org/.&nbsp;</p> <p><strong>Contents</strong></p> <p>There are three tarball (<strong>.tar.gz</strong>) files, one for each of the HCV strain investigated.&nbsp;</p> <p>The contents of each tarball is as follows:</p> <p>1. a source PDB (<strong>.pdb</strong>)&nbsp; file</p> <p>2. <strong>leap.scr</strong> - a script used to create the .prmtop and .inpcrd files</p> <p>3. Two AMBER parameter/topology (<strong>.prmtop</strong>) (one with hydrogen mass repartitioning)&nbsp;and an AMBER&nbsp;coordinate (<strong>.inpcrd</strong>) file&nbsp;</p> <p>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</p> <p>5. Executable <strong>do_md</strong> that performed&nbsp;all the minimisation, relaxation and equilibration steps</p> <p>6. File <strong>parmed.txt</strong>&nbsp;used to repartition the hydrogen atom mass (for the unglycosylated simulations)</p> <p>7. control file <strong>prod.ctl</strong> used for the production run&nbsp;</p> <p>8. Executable <strong>run_prod</strong>&nbsp;that was used to perform&nbsp;the production run</p> <p>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</p> <p>10. Executable <strong>run_short</strong> and <strong>run_short_2</strong>&nbsp;used to carry out the de-correlated&nbsp;production runs.</p> <p>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&nbsp;over 2GB.</p>