SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)
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Micholas Dean Smith | Oak Ridge National Laboratory
David M Rogers | Oak Ridge National Laboratory
Josh Vermaas | Oak Ridge National Laboratory
Jeremy C Smith | Oak Ridge National Laboratory/UTK
Description
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).
Funding Information
DOE Contract Number
DE-AC05-00OR22725Originating Research Organization
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States);The University of Tennessee, KnoxvilleSponsoring Organization
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.Details
Release Date
January 20, 2021Subject
60 APPLIED LIFE SCIENCES, 99 GENERAL AND MISCELLANEOUSKeywords
SARS CoV-2, coronavirus, protein, simulation, gromacs, molecular dynamicsDataset
Dataset Type
SM Specialized MixSoftware
GROMACS (version 2020.1 or greater); VMD (optional)Cite This Dataset:
Smith, M., Rogers, D., Vermaas, J., Smith, J. (2021). SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters). Oak Ridge National Laboratory. https://doi.org/10.13139/OLCF/1650650.
Acknowledgements
This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Advanced Scientific Computing Research programs in the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.