Torsion angles molecular dynamics

Stein EG, Rice LM, Brunger AT. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 1997 124 154-164. 

A set of orientational restraint potentials has been developed for solid-state NMR observables including N chemical shift and N- H dipolar coupling. Torsion angle molecular dynamics (MD) simulations with available experimental N chemical shift and N- H dipolar coupling as target values have been performed to determine orientational information of four membrane proteins and to model the structures of some of these systems in oligomer states. The results suggest that incorporation of the orientational restraint potentials into MD simulations provides an efficient... 

Armen RS, Chen J, Brooks CL III (2009) An evaluation of explicit receptor flexibility in molecular docking using molecular dynamics and torsion angle molecular dynamics. J Chem Theory Comput 5(10) 2909-2923. doi 10.1021/ct900262t... 

Figure 2 Radius of convergence of different refinement methods applied to test refinements with realistic errors added to the initial model. Backbone atom r.m.s. coordinate deviations after refinement are plotted against the starting backbone atom r.m.s. coordinate deviation. The thin dashed line corresponds to refinement by conjugate gradient minimization, the thin solid line corresponds to refinement by slow-cooling simulated annealing using Cartesian molecular dynamics. The thick dot-dashed line corresponds to the average result from ten constant temperature torsion angle molecular dynamics refinements the thick solid line corresponds to the best result from each series of ten refinements...

Figure 5 Average structures from refinements of the DNA dodecamer (CGCGPATTCGCG). (a) Structure produced using Cartesian molecular dynamics simulated annealing, (b) Structure produced using torsion angle molecular dynamics...

You can include geometric restraints—for interatomic distances, bond angles, and torsion angles—in any molecular dynamics calculation or geometry optim i/.ation. Here are some applications of restrain ts ... 

Example Yon can monitor improper torsion angles to determine wh ich side of a substrate m olecn le faces the active site of a protein. Select three atoms on the substrate molecule and a fourth in the active site. These atom s define an improper torsion angle. Save th is selection as a named selection. Then observe a plot of this improper torsion angle (in the Molecular Dynam ics Results dialog... 

Fig. 7.15 The variation in torsion angles can be effectively represented as a series of dials, where the time corresponds to the distance from the centre of the dial. Data from a molecular dynamics simulation of an intermolecular complex between the enzyme dihydrofolate reductase and a triazine inhibitor [Leach and Klein 1995].

You can add restraints to any molecular mechanics calculation (single point, optimization or dynamics). These might be NMR restraints, for example, or any situation where a length, angle, or torsion is known or pre-defined. Restraints with large force constants result in high frequency components in a molecular dynamics calculation and can result in instability under some circumstances. 

The size of the atoms and the rigidity of the bonds, bond angles, torsions, etc. are determined empirically, that is, they are chosen to reproduce experimental data. Electrons are not part of the MM description, and as a result, several key chemical phenomena cannot be reproduced by this method. Nevertheless, MM methods are orders of magnitude cheaper from a computational point of view than quantum mechanical (QM) methods, and because of this, they have found a preferential position in a number of areas of computational chemistry, like conformational analysis of organic compounds or molecular dynamics. 

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