Published August 28, 2023
| Version v1
Dataset
Open
MD simulations of the Sec61/TRAP/ribosome complex Amber force fields
Creators
- 1. Institute of Biotechnology, University of Helsinki
Description
Simulation data for the Sec61/TRAP/ribosome complex embedded in an ER membrane mimic. Simulations are performed using GROMACS and with the all-atom Amber family of force fields. The uploaded trajectory (xtc) contains the coordinates stored every 2 ns of the 2-µs-long simulations. The output energy file (edr), run input file (tpr), and the continue point (cpt) at 2 µs are provided.
All required input files are also provided to regenerate the run input file: initial structures (gro), index files (ndx), topologies (top and itp), and the 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
Files
(4.9 GB)
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md5:9f7456dd1009298438d77da098d3d754
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1.1 kB | Download |
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md5:838708d3d047dc0979bd5e9c3b308b82
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28.9 MB | Download |
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md5:21b38add0aa7aafe16a8e659fe23ccd2
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139.2 MB | Download |
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md5:257aac482288fc67071397df4bec85b4
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18.8 MB | Download |
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md5:d6fa69513d38a1b13f05082ee69a06c6
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990 Bytes | Download |
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md5:a436f015dad20a96be70d28b37e927bf
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4.6 GB | Download |
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md5:a2f9dac57599e08dd5e4d2f4097eadff
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83.0 MB | Download |
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md5:4d866373b1252c8df1675a1880c9c142
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25.0 MB | Download |
Additional details
Funding
- Chemical biology approach for dissecting ER proteostasis 338836
- Research Council of Finland
- A Molecular View on the Health Hazards of Ultrafine Particulate Matter 338160
- Research Council of Finland
- Structures of Endogenous of Macromolecular Assemblies / Consortium: SEMMA 314672
- Research Council of Finland