Application of Molecular Modeling Packages

Published FF parameters for MM (Jalaie and Lipkowitz, 2000 Osawa and Lip-kowitz, 1995) and software for molecular modeling (Boyd, 1995) have been compiled. Some of the MM programs applicable to molecular modeling of biomolecules are listed in Table 14.1. 

All of these programs are available for Unix operating system. Most of the Windows versions are incorporated into commercial molecular modeling packages such as MM in Chem3D of CambridgeSoft (http //www.camsoft.com), AMBER and CHARMm in HyperChem of HyperCube (http //www.hyper.com), and SYBYL 

TABLE 14.1. Molecular Modeling Programs of Biochemical Interest 

AMBER University of California, San Francisco/HyperChem Weiner et al. (1984) 

MACROMODEL Columbia University Chemistry, Columbia University 

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Hypercube, Inc. at http //www.hyper.com offers molecular modeling packages under the HyperChem name. HyperChem s newest version, Hyper-Chem Release 7.5, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum Mechanics. The DFT engine includes four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (CHARMM) force field. Release 7.5 of HyperChem updates... 

Since the report for the initial four elements, AMI parameterizations for B, F, Mg, Al, Si, P, S, Cl, Zn, Ge, Br, Sn, I, and Hg have been reported. Because AMI calculations are so fast (for a quantum mechanical model), and because the model is reasonably robust over a large range of chemical functionality, AMI is included in many molecular modeling packages, and results of AMI calculations continue to be reported in the chemical literature for a wide variety of applications. 

Before closing this section it should be mentioned that most of the methods discussed above can be solved using commercially available programs such as symbolic computation (Mathematica, Maple, or Mathcad 3.0), equation solvers (TK Solver Plus or Mathcad 3.0), spreadsheets (e.g., Lotus 123, Quattro Pro, Microsoft Excel, or Wingz), simulators (Extend or Stella), or Microsoft FORTRAN 5.0. For example, one can introduce the idea of molecular mechanics on model systems using a spreadsheet. Actual applications of molecular mechanics are much better carried out on a software package designed for that purpose, however. 

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