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

Background

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/. 

Contents

There are three tarball (.tar.gz) files containing the core simulation data: 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 (.pdb)  file

2.     Five AMBER trajectory (.nc) files for five independent MD simulations, numbered 1 to 5. Note: each of these files is over 2GB.

There is an additional tarball containing the control files and scripts used for running the MD simulations:

1.     Multiple control (.ctl) files numbered 1 to 10 that are used to minimize (min prefix), relax (rel prefix) and equilibrate (equ prefix) the model

2.     Executable do_md that performed all the minimisation, relaxation and equilibration steps

3.     control file prod.ctl used for the production run 

4.     Executable run_prod that was used to perform the production run

5.     Two control files (prod_short.ctl and prod_short_2.ctl) for the short runs used to de-correlate the simulation for the independent runs

6.     Executable run_short and run_short_2 used to carry out the de-correlated production runs.