We present an approach to optimize force field parameters using time-dependent data from NMR relaxation experiments. To do so, we scan parameters in the dihedral angle potential energy terms describing the rotation of the methyl groups in proteins and compare NMR relaxation rates calculated from molecular dynamics simulations with the modified force fields to deuterium relaxation measurements of T4 lysozyme. We find that a small modification of C^(?) methyl groups improves the agreement with...
[NMR paper] Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations
Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations
Proteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side-chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (average block selection using relaxation data with entropy restraints), can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to...
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nmrlearner
Journal club
0
07-23-2021 01:54 AM
A simple approach for reconstruction of non-uniformly sampled pseudo-3D NMR data for accurate measurement of spin relaxation parameters
A simple approach for reconstruction of non-uniformly sampled pseudo-3D NMR data for accurate measurement of spin relaxation parameters
Abstract
We explain how to conduct a pseudo-3D relaxation series NUS measurement so that it can be reconstructed by existing 3D NUS reconstruction methods to give accurate relaxation values. We demonstrate using reconstruction algorithms IST and SMILE that this 3D approach allows lower sampling densities than for independent 2D reconstructions. This is in keeping with the common finding that higher dimensionality...
[NMR paper] CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
J Comput Chem. 2013 Jul 6;
Authors: Huang J, Mackerell AD
Abstract
Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR...
15N-NMR relaxation data of protein fitting with Modelfree anaylsis
HELLO Every one
my question is ,, i fitted my data on modelfree ,,i get output file mfout
which one is best value for order parameter (S2, S2F,S2S,) in this two
1- fit value ---
2-sim_value
in these two which one i write in my data
khannmr123
NMR Questions and Answers
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08-11-2011 05:14 PM
[NMR paper] Practical model fitting approaches to the direct extraction of NMR parameters simulta
Practical model fitting approaches to the direct extraction of NMR parameters simultaneously from all dimensions of multidimensional NMR spectra.
Related Articles Practical model fitting approaches to the direct extraction of NMR parameters simultaneously from all dimensions of multidimensional NMR spectra.
J Biomol NMR. 1998 Aug;12(2):277-97
Authors: Chylla RA, Volkman BF, Markley JL
A maximum likelihood (ML)-based approach has been established for the direct extraction of NMR parameters (e.g., frequency, amplitude, phase, and decay rate)...
Fitting Force Field Parameters to NMR Relaxation Data
Linear Mode
