Data for Multiscale simulations reveal TDP-43 molecular level interactions driving condensation
Ingólfsson H.I., A. Rizuan, X. Liu, P. Mohanty, P.C.T. Souza, S.J. Marrink, M.T. Bowers, J. Mittal, J. Berry. Multiscale simulations reveal TDP-43 molecular level interactions driving condensation. Biophysical Journal, 2023.
Input parameters and models of full-length TDP-43 used in this analysis
Full-length all-atom model of TPD-43 after initial equilibration: AA_confout_200ns_protein_rna.pdb
General Martini 3.0.0 input parameters: martini_v300.zip (from the Martini portal http://cgmartini.nl/index.php/force-field-parameters/particle-definitions)
TDP-43 Martini 3 parameters, scaled Martini 3 force fields and GROMACS simulation options files: resources.zip
TDP-43 Martini 3 example simulations files. Coordinate files are provided after initial equilibrium and after 10 microseconds of simulation. Simulation topology files (.top) are also available:
- One protein (protein only): TDP43_full_length_1_protein_only.zip
- One protein with RNA (protein only): TDP43_full_length_1_rna_protein_only.zip
- Two proteins (full system, including water and ions): TDP43_full_length_2_full_system.zip
- Assembly with 24 proteins (full system, including water and ions): TDP43_full_length_24_full_system.zip
Copyright (c) 2023, Lawrence Livermore National Security, LLC.
Produced at the Lawrence Livermore National Laboratory
Written by Helgi I. Ingolfsson ingolfsson1@llnl.gov
Release number LLNL-MI-856519.
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