Model-building program

General checks for the normality of torsion angles, bond angles, bond lengths, etc. [62-64] are good controls for the quality of experimentally determined structures, but are less suitable for the evaluation of models because the better model-building programs simply do not make these kinds of errors. 

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. 

Williams HP (1997) Model Building in Mathematical Programming, 3rd Edition, John Wiley. 

Williams, H. (1999) Model building in Mathematical Programming, Wiley, New York. 

In this fashion, we can build up a hierarchy of basic types and operators—not only the syntactic definitions but also their meanings And because the basics can be different for different modeling and programming languages—for example, not all have exactly the same idea of the passage of time—different packages can be supplied for users of different dialects and can be referenced as stereotypes. 

Build a model for each of the following compounds. Use a molecular model kit or a chemical modelling computer program. 

XtalView This is another excellent program for model building. It is available at http //www.sdsc.edu/ CCMS/Packages/XTALVIEW/xtalview.html. 

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