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

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. The GLYCAM_06j-1 force field was used for the simulations of the glycosylated E2. All software is available from http://ambermd.org/. 

Contents

There are three tarball (.tar.gz) files, one for each of the HCV strain investigated. 

The contents of each tarball is as follows:

1. a source PDB (.pdb)  file

2. leap.scr - a script used to create the .prmtop and .inpcrd files

3. Two AMBER parameter/topology (.prmtop) (one with hydrogen mass repartitioning) and an AMBER coordinate (.inpcrd) file 

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

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

6. File parmed.txt used to repartition the hydrogen atom mass (for the unglycosylated simulations)

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

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

9. 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

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

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