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

Smith, Micholas Dean; Rogers, David M; Vermaas, Josh; Smith, Jeremy C

doi:10.13139/OLCF/1650650

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

Dataset
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Abstract

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).

Authors:

Smith, Micholas Dean; Rogers, David M; Vermaas, Josh; Smith, Jeremy C

ORNL-OLCF

Publication Date:: Tue Jan 19 23:00:00 EST 2021

DOE Contract Number:: AC05-00OR22725

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); The University of Tennessee, Knoxville

Sponsoring Org.:: 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.

Subject:: 60 APPLIED LIFE SCIENCES; 99 GENERAL AND MISCELLANEOUS; SARS CoV-2, coronavirus, protein, simulation, gromacs, molecular dynamics

OSTI Identifier:: 1650650

DOI:: https://doi.org/10.13139/OLCF/1650650

Citation Formats


                    Smith, Micholas Dean, Rogers, David M, Vermaas, Josh, and Smith, Jeremy C. SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters).  United States: N. p., 2021. 
        Web.  doi:10.13139/OLCF/1650650.

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                    Smith, Micholas Dean, Rogers, David M, Vermaas, Josh, & Smith, Jeremy C. SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters).  United States.  doi:https://doi.org/10.13139/OLCF/1650650

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                    Smith, Micholas Dean, Rogers, David M, Vermaas, Josh, and Smith, Jeremy C. 2021.  
"SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)".  United States.  doi:https://doi.org/10.13139/OLCF/1650650.  https://www.osti.gov/servlets/purl/1650650. Pub date:Tue Jan 19 23:00:00 EST 2021

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@article{osti_1650650,

  title        = {SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)},

  author       = {Smith, Micholas Dean and Rogers, David M and Vermaas, Josh and Smith, Jeremy C},

  abstractNote = {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).},

  doi          = {10.13139/OLCF/1650650},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue Jan 19 23:00:00 EST 2021},

  month        = {Tue Jan 19 23:00:00 EST 2021}

}

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DOI: https://doi.org/10.13139/OLCF/1650650

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