AMBER molecular structure determination

The molecular dynamics for NMR structure determination and the torsion angle dynamics were extensively reviewed by Giintert.35 The method was also reviewed by Clore and Schwieters.20 The molecular dynamics programs, e.g., CHARMM,42 AMBER,43 and GROMACS44 can be used for the structure determination. XPLOR,38 its successor CNS,45 and XPLOR-NIH12... 

Semiempirical functionals intend to reproduce accurate properties using as many semiempirical parameters as needed. The concept of these functionals may be based on the force fields of molecular mechanics, for example, CHARmm (Brooks et al. 1983) and Amber (Pearlman et al. 1995), which have been established to determine the structures of biomacromolecules such as folded proteins. In most cases, the development of such force fields focuses only on constructing potentials to yield highly accurate molecular structures. Likewise, semiempirical functionals have been developed to provide highly accurate properties. Note, however, that... 

Ionic liquids share parts of their molecular architectures with molecules that had been parameterized by existing force-field frameworks (AMBER, OPLS, CHARMM, etc.) for example imidazolium rings are present in hystidine, an amino acid. However ionic liquids have one essential difference they are composed of ions, and although they may be built by the same functional groups, the distributions of electrostatic charge will be specific. In order to represent correctly the structure and interactions of these new compounds, the sets of parameters that determine charge distributions and conformations (at the least) had to be developed for this class of substances. 

Figure 7 Three-dimensional structure of DNA hairpin d(GCGAAGC) determined using NMR data obtained on a C- and N-labeled molecule. NOE, dihedral, and RDC restrains were applied to refine the structure using molecular dynamics simulations using AMBER 7.0 software package.

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