SIRAH-CoV2 initiative: Spike D614G mutation (introduced on PDB id:6XR8)

This dataset contains the raw data of a coarse-grained molecular dynamics simulation of the D614G mutant of Spike protein from SARS-CoV-2. The initial coordinates correspond to the PDB structure 6XR8, where the coordinates of the side chain of Aspartate 614 were deleted to produce a Glycine. Missing loops were introduced with Swiss-Model (https://swissmodel.expasy.org). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan parameters correspond to those reported by Garay et at.2020. 

The files spike_D614G_SIRAHcg_rawdata_0-2us.tar, spike_D614G_SIRAHcg_rawdata_2-4us.tar, spike_D614G_SIRAHcg_rawdata_4-6us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at www.sirahff.com.

Additionally, the file spike_D614G_SIRAHcg_prot_10us.tar contains only the protein coordinates, while spike_D614G_SIRAHcg_prot_10us_skip10ns.tar contains one frame every 10ns. Notice that these two files contain a 10-microsecond trajectory, while the raw data is limited to 6 microseconds because of size restrictions on the database. Raw data from microseconds 6 to 10 is available upon request (see below).

To take a quick look at the trajectory:

1- Untar the file spike_D614G_SIRAHcg_prot_10us_skip10ns.tar

2- Open the trajectory on VMD using the command line:

vmd spike_D614G_SIRAHcg_prot.prmtop spike_D614G_SIRAHcg_prot.ncrst spike_D614G_SIRAHcg_10us_skip10ns.nc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. 

This dataset is part of the SIRAH-CoV-2 initiative.

For further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).