Computer programs AMBER

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 ... 

D. M. Ferguson, G. L. Seibel, and P. A. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comp. Phys. Comm. 91 1 (1995). 

D. Ferguson, G. Seibel, and P. Kollman, Comput. Phys. Commun., 91,1 (1995). AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules. 

To obtain the data presented here, an attempt has been made to keep the queries as general as possible to maximize relevant hits, but specific enough to minimize extraneous hits. A difficulty is that some words used as computer program names (e.g., discover, gaussian, amber, grid) occur in the literature with other meanings, so the queries must constructed with care to obtain as useful data as possible. This difficulty means that some searches may not be strictly comparable to others. Because thousands of hits were obtained in the course of this study, it was impossible to examine each one individually, but sampling was done to make sure that the searches yielded relevant hits. 

These issues are discussed by Comba and Hambley who also provide a detailed account of how to derive FF parameters as do Norrby and Brandt. Computer programs which have been applied to modeling various coordination compounds include versions of MM2 and MM3, SHAPES,and modified versions of MacroModel, CHARMM, AMBER,MOMEC, ... 

Two well-established computer programs for MD simulations are CHARMM [24] and AMBER [219], which implement a similar functional form of the atomistic force field and include a large number of tools for setting up the files required to run an MD simuIatiOTi. 

Table 3 lists chemists who have been most cited in chapters of prior volumes of our book series. Not surprisingly, all those listed are computational chemists, and many have written a chapter for Reviews in Computational Chemistry. It is interesting to notice how frequently the listed individuals are associated with developing a computer program that is well known in the lexicon of computational chemistry AMBER, CHARMM, Gaussian, UHBD, GROMOS, MM2/MM3, ECEPP, BOSS, DGEOM, MOPAC, DOCK, and so forth. 

AMBER is a set of computer programs that use molecular mechanics, molecular dynamics, normal mode analysis, and free energy calculations to simulate accurately the properties of complex molecules and their interactions, both in vacuo and in condensed phases. A detailed description of the history and current form of AMBER has recently been published, so this article will attempt to give an overview of the program and the features which distinguish it from related programs. 

In this context, we would like to emphasize the often blurred distinction between force field , the functional form and parameters, and the computer program used. The force field used by Weiner et al. (often called the AMBER force field ) has been implemented within the TRIPOS, DISCOVER, and MACROMODEL programs. In principle, the Cornell et al. force field, because of its simple functional form, could be implemented within all the programs mentioned above, with only minor modifications required in a few cases. On the other hand, for example, AMBER could not, without major changes, implement the MM4 force field. In our opinion, force field parameters, in contrast to the software in which they are used, must be made available in their entirety when an article using them is published, either in the article or an appendix or through the World Wide Web. A publication is not really science unless its results can be reproduced by others ... 

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