Molecular structure programs structures

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... 

Crystal (we tested Crystal 98 1.0) is a program for ah initio molecular and band-structure calculations. Band-structure calculations can be done for systems that are periodic in one, two, or three dimensions. A separate script, called LoptCG, is available to perform optimizations of geometry or basis sets. 

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. 

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