Molecular mechanics generating parameters

The reference 4 authors discuss criteria that should be applied when describing molecules with these molecular mechanics programs. Some of these are as follows (1) Check the error file for interactions not in the parameter set, because some programs will assign a force constant of zero to unrecognized atom types (2) check all interactions generating >5 kJ/mol of strain to determine, for instance, whether that bond or angle really is that strained or whether there is a parameterization or molecular structure problem and (3) check the... 

We have also added the capabilities of Dr. Hop-finger s CHEMLAB package( ) which can be used to generate new parameters for analysis or can be used in a more qualitative fashion for conformational analysis based on molecular mechanics. 

In summary, quantum mechanics attempts to model the position or distribution of the electrons or bonds, while mtv lecular mechanics attempts to model the positions of the nuclei or atoms. Quantum mechanics calculations are used commonly to generate or verify molecular mechanics parameters. Larger. structures can be studied hy use of molecular mechanics, and with. simulation techniques such as molecular dynamics, the behavior of drugs in solution or even in pas.sage through bilayer membranes can he studied. 

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