Models computer-assisted building

Figure 3. Preferred conformation of pigment 15B determined by computer-assisted model building (MacroModel) and molecular mechanics (MM3) (31).

After selecting a stationary phase and the mobile-phase components, several isocratic experiments are required to build a retention model. A computer-assisted multivariate procedure is often used to find the best combination of the working parameters.Separation selectivity is often monitored by maximum resolvable components in the shortest time at separation of multicomponent samples. 

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... 

There have been a number of model studies on these types of compounds with computational analysis being applied to assist in the understanding of molecular structure and reactivity as well as in the estimation of the potential of molecules to act as high energetic materials or molecular building blocks. 

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. 

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. 

The computational complexity of the configuration problem requires the assistance of a comprehensive decision support system. The decision support system provides not only core services like data integratirai, model building, and model solving, but... 

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 ... 

---