Computer programs ALCHEMY

Molecular mechanics simulations use the laws of classical physics to predict the structures and properties of molecules. Molecular mechanics methods are available in many computer programs, including MM3, HyperChem, Quanta, Sybyl, and Alchemy. There are many different molecular mechanics methods. Each one is characterized by its particular/orce eW. A force field has these components ... 

Energy minimization, ccmformational searching and molecular mechanics were performed using Alchemy 2000 program system from Tripos loaded on a PC Pentium Computer. For molecular mechanics optimization, the MM3 Molecular Mechanics siAroutine with a value of 4.7 for dimethyl formamide dielectric constant, a RMS gradient of 0.05 kCai/A mot and a delta of energy of 0.001 kCai/A was used. 

PCMODEL also reads and writes files imported from many other types of molecular calculation programs (including MM2, MM3, MOPAC, Gaussian, Macromodel, Alchemy, Sybyl, and Chem-3D), so you can create and edit your preferred structure calculation files. Alternatively, you can use the PCM file format, an easily readable, free-format file that maintains all structure information including substructure names and membership, atomic charge, and user-specified minimization parameters. Since these files are ASCII text files, they can be transferred to another computer as input to calculations on another system. 

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