Molecular structure programs

An Intelligent Sketch Pad as Input to Molecular Structure Programs... 

TRINDLE An Intelligent Sketch Pad for Molecular Structure Programs 165... 

Abstract. BERTHA is a 4-component relativistic molecular structure program based on relativistic Gaussian (G-spinor) basis sets which is intended to make affordable studies of atomic and molecular electronic structure, particularly of systems containing high-Z elements. This paper reviews some of the novel technical features embodied in the code, and assesses its current status, its potential and its prospects. 

G. A. Gallup, The CRUNCH Suite of Atomic and Molecular Structure Programs, 2001. ggallup phy-ggallup. unl.edu. 

To recognize which programs can be used for graphical input and visualization of molecular structures... 

The CACTVS molecule editor is a graphical input tool for molecular structures and is free of charge for non-profit use. It can be used as a stand-alone or as a dependent remote program of the CACTVS computation workbench. The software is available for aU platforms (excluding Macintosh systems). 

Many programs exist which can be used to generate and visualize molecular structures. 

Schaeffer H F III (Editor) 1977. Applications of Electronic Structure Theory. New York, Plenum Press. Schaeffer H F III (Editor) 1977. Methods of Electronic Structure Theory. New York, Plenum Press. Stei. art J J P 1990. MOP AC A Semi-Empirical Molecular Orbital Program. Journal of Computer-Aided Molecular Design 4 1-45. 

Rusinko A III, J M Skell, R Balducci, C M McGarity and R S Pearlman 1988. CONCORD A. Program fi the Rapid Generation of High Quality 3D Molecular Structures. St Louis, Missouri, The University < Texas at Austin and Tripos Associates. 

In most programs, it is still possible to input a geometry manually in an ASCII input file. If the geometry is already in a file but of the wrong format, there are several utilities for converting molecular structure files. The most popular of these is the Babel program, which is described in Appendix A. 

If a program is given a molecular structure and told to find a transition structure, it will first compute the Hessian matrix (the matrix of second derivatives... 

AMPAC can also be run from a shell or queue system using an ASCII input file. The input file format is easy to use. It consists of a molecular structure defined either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. 

A semiempirical crystal band structure program, called BZ, is bundled with MOPAC 2000. There is also a utility, referred to as MAKPOL, for generating the input for band structure calculations with BZ. With the use of MAKPOL, the input for band-structure computations is only slightly more complicated than that for molecular calculations. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

PC Model has some features that are not found in many other molecular mechanics programs. This is one of the few programs that outputs the energy given by the force field and the heat of formation and a strain energy. Atom types for describing transition structures in the MMX force field are included. There is a metal coordination option for setting up calculations with metal atoms. There are also molecular similarity and conformation search functions. 

The molecular structure input requires atom types to be assigned, which are not the same from one force field to the next. The input also includes a list of bonds in the molecule. There is not a module to automatically assign atom types. Most of the modules use a Cartesian coordinate molecular structure, except for a few that work with torsional space. The same keyword file is read by all the executables. A little bit of input is obtained by the program either interactively or from an ASCII file piped to standard input, which makes for a somewhat cryptic input file. This system of common input files and the user choosing which executables to run give TINKER the ability to run very sophisticated simulations while keeping the input required for simple calculations fairly minimal within the limitations mentioned here. 

The program was made somewhat less convenient to use by the fact that it does not have a molecule builder. In order to predict chemical shifts, the molecular structure must be built with some other software package and then im-... 

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