Dataset Open Access

SIRAH-CoV2 initiative: SARS-CoV-2 helicase (PDB id:6ZSL)

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

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Helicase protein (PDB id:6ZSL). 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 Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Parameters for Zinc ions are those reported in Klein et al. 2020.

The files 6ZSL_SIRAHcg_rawdata_0-4us.tar, 6ZSL_SIRAHcg_rawdata_4-8us.tar, and 6ZSL_SIRAHcg_rawdata_8-10us.tar contain all the raw information required to visualize (using 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 6ZSL_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6ZSL_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6ZSL_SIRAHcg_10us_prot_skip10ns.tar

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

vmd 6ZSL_SIRAHcg_prot.prmtop 6ZSL_SIRAHcg_prot.ncrst 6ZSL_SIRAHcg_prot_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-CoV2 initiative.

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

Files (14.2 GB)
Name Size
6ZSL_SIRAHcg_10us_prot.tar
md5:22e8bd16ce0559507635058451262ec3
1.7 GB Download
6ZSL_SIRAHcg_10us_prot_skip10ns.tar
md5:3f7048a7d76148fd824d4c92c481ad42
35.7 MB Download
6ZSL_SIRAHcg_rawdata_0-4us.tar
md5:a1d3071a207c432e5b5bb0f2a236d8ca
5.0 GB Download
6ZSL_SIRAHcg_rawdata_4-8us.tar
md5:037c86a29f6a8e143558bc0f81593448
5.0 GB Download
6ZSL_SIRAHcg_rawdata_8-10us.tar
md5:b4f4b7e28ae22cdcd212076a1e468e9c
2.5 GB Download
  • Klein et al. JCIM 2020 (DOI:10.1021/acs.jcim.0c00160)

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

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

  • Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)

208
21
views
downloads
All versions This version
Views 208208
Downloads 2121
Data volume 81.1 GB81.1 GB
Unique views 195195
Unique downloads 99

Share

Cite as