MD simulations of the Sec61/TRAP complex with the Martini 3 force field
Creators
- 1. Institute of Biotechnology, University of Helsinki
Description
Simulation data for the Sec61/TRAP complex, the Sec61 complex, and the TRAP complex in a POPC membrane. Simulations are performed using GROMACS and with the coarse-grained Martini 3 force fields. The proteins are kept restrained in the simulations. The uploaded trajectories (xtc) contain the coordinates stored every 10 ns of the 20-µs-long simulations. The output energy files (edr), run input files (tpr), and the continue points (cpt) at 20 µs are provided.
All required input files are also provided to regenerate the run input files: initial structures (gro), index files (ndx), topologies (top and itp), and the common simulation parameter file (mdp). Details of the setup, simulation, and analysis of the systems is available in the preprint:
https://doi.org/10.1101/2022.09.30.510141
Files
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(2.9 GB)
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Additional details
Funding
- Structures of Endogenous of Macromolecular Assemblies / Consortium: SEMMA 314672
- Research Council of Finland
- A Molecular View on the Health Hazards of Ultrafine Particulate Matter 338160
- Research Council of Finland
- Chemical biology approach for dissecting ER proteostasis 338836
- Research Council of Finland