Amber description

The force fields available are MM2, MM3, AMBER, OPLSA, AMBER94, and MMFF. The asterisk ( ) indicates force fields that use a modification of the original description in the literature. There is support for user-defined metal atoms, but not many metals are predefined. MM2 has atom types for describing transition structures. The user can designate a substructure for energy computation. 

Work on plasmas has roots extending back to the Greeks who found that amber mbbed with various materials tended to attract certain objects. The concept of plasma as the fourth state of matter can be traced to Sir William Crookes (2) in 1879. "So distinct are these phenomena from anything which occurs in air or gas at the ordinary tension, that we are led to assume that we are here brought face to face with Matter in a Fourth state or condition, a condition so far removed from the State of gas as a gas is from a Hquid." This description has been shown to be accurate over many years of experimentation and appHcation of plasmas. 

Natural resins have been collected by hand throughout recorded history and used with minimal processing. They are reported to have been used in the arts, both in paints and for polishing sculptures, as early as 350 BC. Amber, the hardest of these resins, has been used as a gemstone from early Greek history to modem times. The electrical properties of amber were first recorded about 300 BC. Following is a description of commercial natural resins that are available in the United States. 

Some of the above mentioned studies also use two-layer ONIOM QM MM approaches to include the full protein in an MM description. Other examples of QM MM calculations of metal enzymes include heme oxygenase [89], nitrate reductase [90] and peptide deformylase [91]. Finally, we note that the ONIOM (I IF Amber) potential energy surface has been directly used in a molecular dynamics study (ONIOM/MD) of cytidine deaminase [92],... 

MD simulations provide a detailed insight in the behavior of molecular systems in both space and time, with ranges of up to nanometers and nanoseconds attainable for a system of the size of a CYP enzyme in solution. However, MD simulations are based on empirical molecular mechanics (MM) force field descriptions of interactions in the system, and therefore depend directly on the quality of the force field parameters (92). Commonly used MD programs for CYPs are AMBER (93), CHARMM (94), GROMOS (95), and GROMACS (96), and results seem to be comparable between methods (also listed in Table 2). For validation, direct comparisons between measured parameters and parameters calculated from MD simulations are possible, e.g., for fluorescence (97) and NMR (cross-relaxation) (98,99). In many applications where previously only energy minimization would be applied, it is now common to perform one or several MD simulations, as Ludemann et al. and Winn et al. (100-102) performed in studies of substrate entrance and product exit. 

Perez A, Marchan I, Svozil D et al (2007) Refinement of the AMBER force field for nucleic acids improving the description of alpha/gamma conformers. Biophys J 92(11) 3817-3829... 

I have tried to avoid the popular terminology used for some of the materials. For example, Baltic ambers have various descriptions in different countries, such as bony or turbid , and a certain colour of coral is sometimes called angel skin . I have felt it best to rely on descriptions instead of the popular names which can be confusing. Similarly, the words imitation and simulant are used instead of the popular expression faux . The exception is the word organics , which I use freely, instead of the more correct, but rather long, materials of organic origin . 

Stacked NA base pairs AMBER 4.1 with the force field of Cornell et al [16] best reproduces the ab initio stabilization energies and geometries. The success of the Cornell et al force field is probably due to the derivation of atomic charges. It must be also mentioned that this force field provides a better description of interaction energies of NA base pairs than any semiempirical quantum chemical method or even nonempirical ab initio technique of a lower quality than that of the MP2 procedure (DFT or ab initio HF methods). 

It is beyond the scope of this short review to list every available molecular mechanics program. Only a selected few programs are mentioned here, without descriptive details of the potential functions, minimization algorithms, or comparative evaluations. Both the CHARMM and AMBER force fields use harmonic potential functions to calculate protein structures. They were developed in the laboratories of Karplus and Kollman, respectively, and work remarkably well. The CFF and force fields use more complex potential functions. Both force fields were developed in commercial settings and based extensively or exclusively on results obtained from quantum mechanics. Unlike the other molecular mechanics methods, the OPLS force field was parameterized by Jorgensen to simulate solution phase phenomena. 

Standard molecular mechanics (MM) methods (e.g. the popular force fields developed for AMBER, CHARMM and GROMOS decribed in Section 2 above) provide a good description of protein structure and dynamics, but cannot be used to model chemical reactions. This limitation is due their simple functional forms (e.g. harmonic terms for bond stretching) and inability to model changes in electronic polarization (because of the invariant point partial atomic charge used by these molecular mechanics methods to represent electrostatic interactions). 

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