Assisted Model Building with Energy Refinement

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

AMBER (assisted model building with energy refinement) a molecular mechanics force field... 

In conjunction with a study on the reactivity of dimeric quinone me-thides, Elder et al. (56) examined the physical and electronic structure of guaiacylglycerol-/ -coniferyl ether, which is substituted in a manner representative of the lignin polymer. Calculations were performed using AMBER (Assisted Model Building with Energy Refinement) (24), which is a force-field method, and the energetic minimum was determined to be a folded structure similar to that reported by Gravitis and Erins (55). 

AMBER Assisted model building with energy refinement... 

Weiner, P.K. and Kollman, P.A. (1981) AMBER Assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem. 2, 287-303. 

P. Weiner and P. Kollman, J. Comput. Chem., 2, 287 (1981). AMBER Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions. 

Assisted Model Building with Energy Refinement refers to a MM force field for the simulation of biomolecules and a package of molecular simulation programs. 

Wei reported radius- and chirality-dependent conformations of PE on CNT interfaces by MD with the AMBER (assisted model building with energy refinement) force field. ... 

The kind of energy terms, their functional form, and how carefully (number, quality, and kind of reference data) the parameters were derived determine the quality of a force field. Accurate force fields exist for organic molecules (e.g., MM2, MM3), but more approximate force fields (e.g., with fixed bond distances) optimized for computational speed rather than accuracy [e.g., AMBER (assisted model building with energy refinement), CHARMM (chemistry at Harvard molecular mechanics), GROMOS (Groningen molecular simulation)] are the only practical choice for the treatment of large biomolecules. The type of molecular system to be smdied determines the choice of the force field. 

Assisted Model Building with Energy Refinement ANN... 

The computer software and force fields referred to as AMBER (Assisted Model Building with Energy Refinement) are the most popular of those designed for a wide class of biomolecules, including proteins and nucleic acids. The first description of the computer program AMBER appeared in 1981 (Weiner and Kollman 1981), and the first detailed specification of the force field was published 3 years later (Weiner et al. 1984). The force field contained the usual minimalist ... 

AMBER = assisted model building with energy refinement force field CHARMM = chemistry at Harvard macromolecu-lar mechanics force field MP4SDQ = Mpller-Plesset fourth-order perturbation theory with corrections for single, double, and quadruple excitations OPLS = optimized potentials for liquid simulation force field TZP = triple-zeta -f polarization. 

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