Published April 25, 2020 | Version SIRAH version 2.2, Amber18
Dataset Open

SIRAH-CoV2 initiative: Papain-like Protease (PDB id:6W9C)


This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Papain-like protease in its APO form with Zn ions bound (PDB id: 6W9C). 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. Zinc ions were parameterized as reported in Klein et al. 2020.

The files 6W9C_SIRAHcg_rawdata_0-5us.tar,  6W9C_SIRAHcg_rawdata_5-10us.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

Additionally, the file 6W9C_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W9C_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6W9C_SIRAHcg_10us_prot_skip10ns.tar

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

vmd 6W9C_SIRAHcg_prot.prmtop 6W9C_SIRAHcg_prot.ncrst -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 Florencia Klein ( or Sergio Pantano (


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Additional details


  • Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)
  • Machado & Pantano. Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)
  • Machado & Pantano. JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)
  • Klein et al. JCIM, 2020 (DOI:10.1021/acs.jcim.0c00160)