Molecular software

W. F. Van Gimsteien and H. I. Berendsen. BlOMOS, Bio molecular Software, Laboratory of Physical Chemistry, University of Groningen, Groningen, The... 

This method has been used extensively in the literature for the calculation of molecular hyperpolarizabilities. The calculations employed here utilized the MOPAC and ZINDO methods within the 4.0.1 CAChe Worksystem (Oxford Molecular) software package. MNDO-AM1 method and parameterization M. J. S. Dewar and M. L. McKee, J. Am. Chem. Soc., 1977, 99, 5231. Oscillator strengths were calculated using the ZINDO method. 

In 2000, the Oxford Molecular software businesses were acquired by Pharmacopeia Inc., which already had created a sound scientihc software segment with the acquisition of Molecular Simulations Inc. and Synopsys Scientihc Systems Ltd. Pharmacopeia combined its software subsidiaries in June 2001 to form Accelrys, which separated from Pharmacopeia in 2004. 

The CAChe software packages from Oxford Molecular webpage http //www.oxmol.com/aetinfo/eduf... 

A comprehensive and up-to-date introduction to the ideas of molecular dynamics and Monte Carlo, with statistical mechanical background, advanced teclmiques and case studies, supported by a Web page for software download. 

The full dynamical treatment of electrons and nuclei together in a laboratory system of coordinates is computationally intensive and difficult. However, the availability of multiprocessor computers and detailed attention to the development of efficient software, such as ENDyne, which can be maintained and debugged continually when new features are added, make END a viable alternative among methods for the study of molecular processes. Eurthemiore, when the application of END is compared to the total effort of accurate determination of relevant potential energy surfaces and nonadiabatic coupling terms, faithful analytical fitting and interpolation of the common pointwise representation of surfaces and coupling terms, and the solution of the coupled dynamical equations in a suitable internal coordinates, the computational effort of END is competitive. 

T. G. Mattson and G. R. Shanker, Portable molecular dynamics software for parallel computing , ACS Symposium Series 592, 133-50. 

Early implementations of the CIP rules for computer detection and specification of chirality were described for the LHASA [105], CHIRON [106], and CACTVS [107] software packages. Recently, several commercial molecular editors and visualizers (e.g., CambridgeSoft s ChemOffice, ACD s I-Lab, Accelrys WebLab, and MDL s AutoNom) have also implemented the CIP rules. 

In recent years, the rapid development of low-budget 3D-capablc graphics cards makes it possible to visualize molecular models with standard PC systems. Some molecular modeling software, which was once available only for workstations, is now also offered for PCs [198]. 

The most important feature of editing software is the option to save the structure in standard file formats which contain information about the structure (e,g., Mol-filc. PDB-filc). Most of these file formats arc ASCII text files (which can be viewed in simple text editors) and cover international standardized and normalized specifications of the molecule, such as atom and bond types or connectivities (CT) (see Section 2,4). Thus, with these files, the structure can be exchanged between different programs. Furthermore, they can seiwe as input files to other chemical software, e.g, to calculate 3D structures or molecular properties. 

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). 

Chcm3D is much more than a molecule viewer. This autonomous software module from the ChemOffice package provides simple molecule editor tools to create structures, but is mainly used as a molecular modeling tool. 

To get an overview of the currently available software for molecular mechanics calculations with their strengths, weaknesses, and application areas... 

Software used in molecular modeling and molecular dynamics http //www.akpcc. 

The chirality code of a molecule is based on atomic properties and on the 3D structure. Examples of atomic properties arc partial atomic charges and polarizabilities, which are easily accessible by fast empirical methods contained in the PETRA package. Other atomic properties, calculated by other methods, can in principle be used. It is convenient, however, if the chosen atomic property discriminates as much as possible between non-equivalent atoms. 3D molecular structures are easily generated by the GORINA software package (see Section 2.13), but other sources of 3D structures can be used as well. 

HyperChem should not he viewed as a black box that computes on ly wb at its design ers th ougb L correct, tthasan open architecture that makes it possible to customize it many ways. As far as is possible, the parameters of molecular mechanics and semi-empir-ieal calculations are in the user s baruis. As the tech n ic ues of software engineering advance and onr expertise in building new... 

Molecular modelling used to be restricted to a small number of scientists who had access to the necessary computer hardware and software. Its practitioners wrote their own programs, managed their own computer systems and mended them when they broke down. Today s computer workstations are much more powerful than the mainframe computers of even a few years ago and can be purchased relatively cheaply. It is no longer necessary for the modeller to write computer programs as software can be obtained from commercial software companies and academic laboratories. Molecular modelling can now be performed in any laboratory or classroom. 

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