Available Force Fields

Many versions of force field parameters exist, distinguished by ordinal number. All-atom and united-atom versions exist. 

Version of CHARMM somewhat extended and made available in Acccirys software products. 

CVFF is the original CFF versions are identified by trailing year digits. Bond stretching can be modeled with a Morse potential. 

Bond stretching can be modeled with a Morse potential. 

Computes only non-bonded interactions for fixed structures. Versions identified by /(ordinal number) after name. 

Sometimes referred to as AMBER force fields new versions are first coded in software of that name. All-atom (AA) and united-atom (UA) versions exist. 

The program MacroModel contains many modified versions of other force fields, e.g., AMBER, MM2, MM3, OPLSA.  

PEF95SAC Carbohydrates Based on CFF form. Fabricius, J., Engelsen, S. B., and Rasmussen, K. 1997. J. Carhohydr. Chem., 16, 751.  

There are several excellent publications in the literature which compare force fields, their apphcation areas, and their pros and cons [1-5]. Available force field parameters are published in a comprehensive and very extensive form, e.g., within the R views in Computational Chemistry series [6, 7j. 

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E. Extension of Available Force Fields Application to CHARMM... 

Halgren, T. A. (1999) MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and intermolecular-interaction energies and geometries. J. Comput. Chem. 20, 730-748. 

Third, currently available force fields have not been parameterized to handle non-equilibrium forms, in particular, reaction transition states. Note, however, that there is no fundamental reason why this could not be done (using results from quantum chemical calculations rather than experiment as a basis for parameterization). 

The rest of this chapter examines the various components of the molecular energy and the force-field approaches taken for their computation. The discussion is, for the most part, general. At the end of the chapter, a comprehensive listing of reported/available force fields is provided with some description of their form and intended applicability. 

Molecular Mechanics Features ChemSite performs energy minimization and molecular dynamics simulation. Available force fields include Amber, mm2 and the ChemSite s default cm+ force field for accurate calculations with almost any molecule. The program performs real time animation of energy minimization and molecular dynamics simulation with small to medium size molecules. With large molecules such as proteins, movies of molecular dynamics simulations may be recorded to disk and played back for real time animation. 

In principle, the diffusion steps (a) and (e) could be studied through molecular dynamics simulations as long as rehable forces fields are available to describe the zeolite structure and its interaction with the substrates. Also, if the adsorption takes place without charge transfer between the reagents/products and the zeolite, steps (b) and (d) could also be investigated either by molecular dynamics or Monte Carlo simulations. Step (c) however can only be followed by quantum mechanical techniques because the available force fields cannot yet describe the breaking and formation of chemical bonds. 

Contrary to the previous steps of the catalytic process, we cannot use force-field-based techniques because the available force fields are unable to describe the breaking and formation of chemical bonds. Thus, the chemical reaction step must be investigated by quantum mechanical techniques. Right away this imposes some limitations on the size of the cluster to be used in the calculations. In principle, since the catalytic sites are well localized within the zeolite framework, one should expect the chemical reactions to occur at very locahzed points of the zeoUtic structure. Thus, one could think of representing the acid sites by much smaller clusters than the ones used in the diffusion and adsorption studies. 

As seen from Table 2.2 there are a large number of possible compounds for which there are no parameters, and for which it is then impossible to perform force field calculations on (a good listing of available force field parameters can be found in ref. 22. Actually the situation is not as bad as it would appear from Table 2.2. Although only 0.2% of the possible combinations for the torsional constants have been parameterized, these encompass the majority of the chemically interesting compounds. It has been estimated that 20% of the 15 million known compounds can be modelled by... 

MM methods have the advantage that they are much faster than the more robust quantum chemical methods. However, as outlined in a recent review article by Ryde [4], MM methods only yield good bond lengths and angles when the force fields are specifically parameterized for the class of chemical system under consideration. While it is common to describe orthodox protein chains reliably via this approach, available force fields often poorly describe unusual features including substrates, inhibitors, metal sites, and unusual protein conformations. To account for these problems many successful examples were shown by Ryde in which hybrid approaches involving simultaneous application of quantum mechanics (QM) and... 

Structure analysis begins with building a trial model [47]. The radial distribution curve can be very useful for this purpose. From the positions of the peaks one has trial values of rjj and horn their half widths one can estimate trial values of /y (see Fig. 3). Earlier practice was also to take the initial values for the amplitudes of vibration from similar molecules [48-52], however, at the present time the amplitudes are calculated from the available force fields (see more in Section IV.A.). 

Molecular mechanics (force field) calculation is the most commonly used type of calculation in computational medicinal chemistry, and a large number of different force fields have been developed over the years. The results of a molecular mechanics (MM) calculation are highly dependent on the functional forms of the potential energy functions of the force field and of the quality of their parameterization. Thus in order to obtain reliable computational results it is crucial that the merits and limitations of the various available force fields are taken into account. In this chapter, the basic principles of force-field calculations are reviewed, and a comparison of calculated and experimental conformational energies for a wide range of commonly used force fields is presented. As quantum mechanical (QM) methods have undergone a rapid development in the last decade, we have also undertaken a comparison of these force fields with some commonly employed QM methods. The chapter also includes a review of force fields with respect to their abilities to calculate intermolecular interactions. 

Native force field, x = available force field. 

Currently available force fields for proteins contain significant deficiencies (see Sec. 17.5). 

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