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Published November 17, 2020 | Version SIRAH 2.3, Amber18
Dataset Open

SIRAH-CoV2 initiative: RBD triple glycosylated at Asn331, 343, and 481 from PDB structure 6XEY

Description

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of a Spike's RBD from SARS-CoV2 glycosylated at Asn331, 343, and 481 with Man9 glycosylation trees. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6XEY. Missing loops and glycosylation trees were added with CHARMM-GUI (http://www.charmm-gui.org). 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. Glycan parameters correspond to those reported by Garay et al.

The files 6XEY-RBD-3Man9_SIRAHcg_0-4us.tar,  6XEY-RBD-3Man9_SIRAHcg_4-8us.tar, and 6XEY-RBD-3Man9_SIRAHcg_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 6XEY-RBD-3Man9_SIRAHcg_glycoprot_10us.tar contains only the protein coordinates, while 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6XEY-RBD-3Man9_SIRAHcg_glycoprot_skip10ns.tar

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

vmd 6XEY-RBD-3Man9_SIRAHcg_glycoprot.prmtop 6XEY-RBD-3Man9_SIRAHcg_glycoprot.ncrst 6XEY-RBD-3Man9_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-CoV2 initiative.

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

Files

Files (12.0 GB)

Name Size Download all
md5:d674e8fd5383dd5f82048a8679d9545a
4.5 GB Download
md5:d17b2064188c161064a47f24d620a3ce
4.5 GB Download
md5:30b8771e348d6ebf70c9db9555c69d7e
2.2 GB Download
md5:439d491302b3079aa898033decf3c0b9
745.5 MB Download
md5:cdc195777f5313ae3ca07676ce432eea
15.6 MB Download

Additional details

References

  • 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)
  • Garay et al. 2020 (DOI:10.1101/2020.12.18.423446v1)