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Published April 10, 2020 | Version SIRAH version 2.2, Amber18
Dataset Open

SIRAH-CoV2 initiative: NSP15 Endonuclease (PDB id:6W01)

Description

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Endopeptidase NSP15 in its APO form (PDB id: 6W01, Bioassembly 1). 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

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 file 6W01_SIRAHcg_10us_prot.tar contain only the protein coordinates, while 6W01_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

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

Files (25.0 GB)

Name Size Download all
md5:cf3ad9222199d6e075ecf93c3cc48318
6.1 GB Download
md5:b4af32a4077ad515f925e72b54fd5d14
125.4 MB Download
md5:08c5e7dcdd16106607df7f90e1fb8b73
18.8 GB Download

Additional details

References

  • Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)
  • Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)