Dataset Open Access

SIRAH-CoV2 initiative: Membrane embedded SARS-CoV-2 ORF3a (PDB id:6XDC)

Exequiel Barrera; Pablo Garay; Florencia Klein; Matías Machado; Martín Soñora; Sergio Pantano

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the SARS-CoV2 ORF3a dimeric transmembrane protein (PDB id: 6XDC, Bioassembly 1) embedded in a membrane patch containing POPE, POPC, and POPS phospholipids in a 2:1:1 proportion. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Barrera et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020

The files 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 files 6xdc_SIRAHcg_rawdata_0-2us.tar, 6xdc_SIRAHcg_rawdata_2-4us.tar, 6xdc_SIRAHcg_rawdata_4-6us.tar, 6xdc_SIRAHcg_rawdata_6-8us.tar, and 6xdc_SIRAHcg_rawdata_8-10us.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 6XDC_SIRAHcg_10us_prot-memb_skip10ns.tar contains only the protein and phospholipids´ coordinates, with one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6xdc_SIRAHcg_10us_prot-memb_skip10ns.tar

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

vmd 6xdc_SIRAHcg_prot-memb.prmtop 6xdc_SIRAHcg_prot-memb.ncrst 6xdc_SIRAHcg_10us_prot-memb_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-CoV2 initiative.

For further details, please contact Exequiel Barrera (ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).

Files (44.5 GB)
Name Size
6xdc_SIRAHcg_10us_prot-memb_skip10ns.tar
md5:d2a0179382c5416f4eb1cb071abcd8f7
1.4 GB Download
6xdc_SIRAHcg_10us_rawdata_0-2us.tar
md5:acd12c51230b55c828d248ba43456999
8.6 GB Download
6xdc_SIRAHcg_10us_rawdata_2-4us.tar
md5:72cfed7b7e4719d0726b1e46f0d1843f
8.6 GB Download
6xdc_SIRAHcg_10us_rawdata_4-6us.tar
md5:b31ee157319c3cda0a83a40f99d3967d
8.6 GB Download
6xdc_SIRAHcg_10us_rawdata_6-8us.tar
md5:338a4c9e3d8a0e16021ca15b762e1a59
8.6 GB Download
6xdc_SIRAHcg_10us_rawdata_8-10us.tar
md5:4edb5374ad9e1daccc234b27ffba95ae
8.7 GB Download
  • Barrera et al. JCTC 2019 (DOI:10.1021/acs.jctc.9b00435)

  • Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)

  • Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)

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