ChemOffice program

Alternately, the commercial molecular modeling software programs such as ChemOffice (http //www.camsoft.com) can be used. The ISIS draw in sketch format (struname.skc) is first converted to ChemDraw format (struname.cdx), which is then transformed into 3D structure (struname.c3d) with Chem 3D (Chapter 14) and saved as PDB format (struname.pdb). 

CS ChemOffice (R) version 4.5 packet program and MM2 method which is implemented in CS ChemOffice (R) version 4.5 were used5. 

The free demonstration program ChemOffice Net (downloadable from www. camsoft.com/) allows one to build molecules containing a maximum of six nonhydrogen atoms and then to do molecular-mechanics energy minimization on them. The internal coordinates and the Cartesian coordinates of the atoms can easily be obtained before and after the energy minimization. These coordinates can then be used as input to an ab initio program. 

ChemOffice a suite of programs incorporating drawing (Chem-Draw, the standard format for chemistry journals) and modeling (Chan3D, using MM and semiempirical methods) with intefaces to other programs. 

Chem3D This program is part of a package of programs called ChemOffice that includes ChemDraw and ChemFinder. It carries out molecular mechanics calculations with the MMR formulas, and can also carry out molecular dynamics calculations, which are basically integration of classical equations of motion. There is a trial version that can be used for two weeks without charge, and there is also a demonstration version that can be used indefinitely but cannot save or print files. Information is available at http //www.cambridgesoft.com. 

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