Refinement energy

The AMBER (Assisted Model Building and Energy Refin emeni) is based on a force field developed for protein and nucleic acid computations by members of the Peter Kollman research group at the... 

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... 

P. A. KoUman and co-workers, AMBER Assisted Model Building and Energy Refinement, Urdversity of CaUforrda, San Erancisco, 1980—present ... 

AMBER (Assisted Model Building and Energy Refinement)... 

Schaumann T, Braun W, Wilthrich K. The program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. Biopolymers 1990 29 679-694. 

Floris, F.M. Tomasi, J. Pascal-Ahuir, J.L., Dispersion and repulsion contributions to the solvation energy refinements to a simple computational model in the continuum approximation, J. Comp. Chem. 1991,12, 784-791... 

Figure 4. Comparison of energy refined structures A, B, and C with NMR structures A", B", and C". (Reproduced with permission from ref. 24. Copyright 1988 Wiley.)...

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... 

Continued Quantum and Molecular Mechanical Simulations, In this technique, a molecular dynamics simulation includes the treatment of some part of the system wilh a quantum mechanical technique. This approach. yMf.MM. is similar to programs that Use quantum mechanical methods to treat the n-systems of the structures in question separately from the sigma framework. The results are combined ai ihe end to render a slructure which is optimized and energy-refined in satisfy both self-consistent field (SCF) and force field energy convergence. 

XPLOR is a modern package of refinement programs that includes powerful procedures for energy refinement by simulated annealing, in addition to more traditional tools like least-squares methods and molecular-replacement searches. The package is available for use on many different computer systems. Simulated annealing for large molecules usually requires supercomputers. 

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. 

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