MD simulation data: An Entropic Safety Catch Controls Hepatitis C Virus Entry and Antibody Resistance

<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. All software is available from http://ambermd.org/. <strong>Contents</strong> There are three tarball (<strong>.tar.gz</strong>) files containing the <strong>core simulation data</strong>: one for wild type (WT), the second for the I438V A524T mutant and the third for the S449P mutant. Each contains: 1. a source PDB (<strong>.pdb</strong>) file 2. 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. There is an additional tarball containing the <strong>control files</strong> <strong>and scripts</strong> used for running the MD simulations: 1. 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 2. Executable <strong>do_md</strong> that performed all the minimisation, relaxation and equilibration steps 3. control file <strong>prod.ctl</strong> used for the production run 4. Executable <strong>run_prod</strong> that was used to perform the production run 5. 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 6. Executable <strong>run_short</strong> and <strong>run_short_2</strong> used to carry out the de-correlated production runs.