10.5281/zenodo.4250123
https://zenodo.org/records/4250123
oai:zenodo.org:4250123
Pablo Garay
Pablo Garay
0000-0001-6604-0329
Institut Pasteur de Montevideo
Exequiel Barrera
Exequiel Barrera
0000-0002-0388-3078
Institut Pasteur de Montevideo
Florencia Klein
Florencia Klein
0000-0003-4099-9907
Institut Pasteur de Montevideo
Matías Machado
Matías Machado
0000-0002-9971-4710
Institut Pasteur de Montevideo
Martín Soñora
Martín Soñora
0000-0003-3872-6117
Institut Pasteur de Montevideo
Sergio Pantano
Sergio Pantano
0000-0001-6435-4543
Institut Pasteur de Montevideo
SIRAH-CoV2 initiative: SARS-CoV-2 helicase (PDB id:6ZSL)
Zenodo
2020
COVID-19
Coarse grain
Molecular Dynamics
Simulation
Drug design
SARS
SIRAH
2020-11-06
eng
10.5281/zenodo.4250122
https://zenodo.org/communities/zenodotus
https://zenodo.org/communities/covid-19
https://zenodo.org/communities/covid19-structure-hub
SIRAH 2.0, Amber 2018, VMD 1.9.3
Creative Commons Attribution 4.0 International
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).