Molecular graphics software packages

In many cases, the coordinates of a molecular structure are available for dovraload on the web, from crystallographic databases (CCDC 2010 ICSD 2009 PDB 2010 Reciprocal Net 2004 Toth 2009) or journal supplements. For relatively small molecules, an initial guess structure can be built using molecular graphics software packages such as molden (2010). 

The disadvantage of molecular mechanics is that there are many chemical properties that are not even defined within the method, such as electronic excited states. Since chemical bonding tenns are explicitly included in the force field, it is not possible without some sort of mathematical manipulation to examine reactions in which bonds are formed or broken. In order to work with extremely large and complicated systems, molecular mechanics software packages often have powerful and easy-to-use graphic interfaces. Because of this, mechanics is sometimes used because it is an easy, but not necessarily a good, way to describe a system. 

A molecular graphics analysis of phthallocyanines in faujasite and VP1-5 is performed with a ChemX-software package from Chemical Design Ltd. Structural data of the molecular sieves and the phthallocyanine complexes were taken from the literature [9-11]-... 

Quantum-chemical calculations were carried out using the LabVision Software Package on a Silicon Graphics Iris Indigo workstation. The molecular orbital semiempirical method was performed using the AMI Hamiltonian. 

With the widespread use of computer graphics interfaces in connection with molecular mechanics calculations and the large number of different molecular mechanics methods available, the major problem today is not how to set up and perform the calculations but which method (or force field) to use for the problem at hand. A related question for the newcomer to molecular modeling is which software to buy. Each software package has at most only a few of the many different force fields, and no one force field is common to all programs. 

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