Molecular modeling commercial packages

The active analog approach was originally in the SYBYL program other major general-purpose molecular modeling commercial packages, however, have implemented their own versions of this technique. 

One can apply the MC technique to the same molecular model, as explored in MD. One can use the same box and the same molecules that experience exactly the same potentials, and therefore the results are equally exact for equilibrium membranes. However, MC examples of this type are very rare. One of the reasons for this is that there is no commercial package available in which an MC strategy is combined with sufficient chemistry know-how and tuned force fields. Unlike the MD approach, where the phase-space trajectory is fixed by the equations of motion of the molecules, the optimal walkthrough phase space in an MC run may depend strongly on the system characteristics. In particular, for densely packed layers, it may be very inefficient to withdraw a molecule randomly and to let it reappear somewhere else in... 

The third stage involves the use of a sophisticated commercial molecular modeling package to explore a more complex chemical problem in a laboratory setting. The problem posed in this stage should also lead the student to increased chemical and physical insight. 

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... 

Chemists talk to each other by drawing pictures, and when nearly two decades ago software became readily available that allowed this to be done electronically, the office environment for chemists changed in a remarkable manner. Well established commercial office packages allow even the most complicated chemical structures to be drawn easily and incorporated into word processing software to use electronic notebooks (see Section B, 3.3.2.6) access databases both external and internally on CD-ROMs integrate into a LIMS use a registration system carry out molecular modelling and determine structure activity relationships [B-ll]. 

The recent developments in the software are phenomenal and they tend to be more and more user-friendly for commercial success. A list of few typical commercial software packages as well as their capabilities are given in Table 1. There are also several extremely useful public domain packages, nevertheless not as user-friendly as commercial packages shown in Table 1, are available in the INTERNET for the molecular modelling enthusiasts. 

For each software package, we give a brief description, the address and telephone number of the supplier, and other pertinent information, such as when a vendor offers more than one program pertinent to molecular modeling. The descriptions are concise overviews, not reviews, and an effort has been made to free the descriptions of commercial embellishments. When possible, a toll-free (U.S.A.) telephone number and/or an electronic mail address is given to make it easier to communicate with the supplier. 

The Chemistry of Life course incorporates active learning methods, including computational molecular modeling, simulations, experiments, and student papers and presentations. As described below, activities have been designed that use commercial software packages to enable students to visualize chemical and physical processes that influence and support life. 

Molecular dynamics consists of the brute-force solution of Newton s equations of motion. It is necessary to encode in the program the potential energy and force law of interaction between molecules the equations of motion are solved numerically, by finite difference techniques. The system evolution corresponds closely to what happens in real life and allows us to calculate dynamical properties, as well as thermodynamic and stmctural functions. For a range of molecular models, packaged routines are available, either commercially or through the academic community. 

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