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

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

Research datakeyboard_double_arrow_right Dataset 18 Aug 2020Publisher:ZenodoFunded by:NNF | unidentified, CF | 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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3x 5 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'

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

4 Research products, page 1 of 1

5x 1 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'

Structural Ensemble of CD4 Cytoplasmic Tail (402–419) Reveals a Nearly Flat Free-Energy Landscape with Local α-Helical Order in Aqueous Solution

Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations

Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets. 1. NMR and MD Characterization of the Complex between the c-Crk N-SH3 Domain and the Peptide Sos