3x 5 µs all-atom MD trajectories; AMBER ff99SB*-ILDN &amp; TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'

Kümmerer, Felix; Orioli, Simone; Harding-Larsen, David; Hoffmann, Falk; Gavrilov, Yulian; Teilum, Kaare; Lindorff-Larsen, Kresten

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ZENODO

Dataset . 2020

License: https://www.gnu.org/licenses/lgpl-3.0-standalone.html

Data sources: Datacite

ZENODO

Dataset . 2020

Data sources: ZENODO

ZENODO

Dataset . 2020

License: https://www.gnu.org/licenses/lgpl-3.0-standalone.html

Data sources: Datacite

3x 5 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'

Research datakeyboard_double_arrow_right Dataset 18 Aug 2020Publisher:ZenodoFunded by:CF | unidentified, NNF | unidentified

Authors: Kümmerer, Felix; Orioli, Simone; Harding-Larsen, David; Hoffmann, Falk; Gavrilov, Yulian; Teilum, Kaare; Lindorff-Larsen, Kresten;

doi: 10.5281/zenodo.3989044 , 10.5281/zenodo.3989043

3x 5 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'

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Abstract

Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024). 3 x 5 µs all-atom MD simulations of T4 Lysozyme Force field: AMBER ff99SB*-ILDN with modified methyl rotation barriers1 Water model: TIP4P/2005 Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters Contains: 3 x GROMACS .xtc trajectory files for 3 independent simulations 3 x corresponding GROMACS .tpr topology files 1 Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2018). Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. The Journal of Physical Chemistry B, 122(19), 5038–5048. https://doi.org/10.1021/acs.jpcb.8b02769

Related Organizations

University of Copenhagen
Denmark
Ruhr University Bochum
Germany

Keywords

T4 Lysozyme, Molecular dynamics simulation, AMBER ff99SB*-ILDN, TIP4P/2005

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