SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)
10.13139/OLCF/1650650A 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 DatasetDataset Properties
Field | Value |
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Authors |
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Project Identifier | BIF128 |
Dataset Type | SM Specialized Mix |
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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.