SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)

10.13139/OLCF/1650650

A set of 24 protein structures/complexes from the SARS CoV-2 proteome and inputs prepared for simulation using the CHARMM36m forcefield in PDB and gromacs formats. Each system contains a pdb and gromacs top and related input files necessary for running a temperature replica-exchange simulation. In addition, we also include: charmm PSF files (generated from the gromacs topology), a list of temperatures at which replica-exchange simulations were done (tempRamp), example gromacs run input mdp files, and initial minimized structures where available (minimized.pdb).

Published: 2021-01-20 15:00:44 Download Dataset

Dataset Properties

Field Value
Authors
  • Smith, Micholas Dean Oak Ridge National Laboratory
  • Rogers, David M Oak Ridge National Laboratory
  • Vermaas, Josh Oak Ridge National Laboratory
  • Smith, Jeremy C Oak Ridge National Laboratory/UTK
Project Identifier BIF128
Dataset Type SM Specialized Mix
Subjects
  • 60 APPLIED LIFE SCIENCES
  • 99 GENERAL AND MISCELLANEOUS
Keywords
  • SARS CoV-2
  • coronavirus
  • protein
  • simulation
  • gromacs
  • molecular dynamics
Software Needed GROMACS (version 2020.1 or greater); VMD (optional)
Originating Organizations Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States);The University of Tennessee, Knoxville
Sponsoring Organizations Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21);Research sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U. S. Department of Energy.
DOE Contract DE-AC05-00OR22725

Acknowledgements

Papers using this dataset are requested to include the following text in their acknowledgements:

*Support for 10.13139/OLCF/1650650 is provided by the U.S. Department of Energy, project BIF128 under Contract DE-AC05-00OR22725. This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility.