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

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

Overview

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 resources

DOE contract number

DE-AC05-00OR22725

Originating research organization

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States);The University of Tennessee, Knoxville

Sponsoring 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

DOI

10.13139/OLCF/1650650

Release date

January 20, 2021

Dataset

Dataset type

SM Specialized Mix

Software

GROMACS (version 2020.1 or greater); VMD (optional)

Acknowledgements

Users should acknowledge the OLCF in all publications and presentations that speak to work performed on OLCF resources:

This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

Keywords

SARS CoV-2,
coronavirus,
protein,
simulation,
gromacs,
molecular dynamics