Molecular Modeling - Mapping Biochemical State Space

Molecular Modeling — Mapping Biochemical State Space 

Is further modification of the Ramachandran plot dependent on the overall volume of the R group Why or why not  

Propose an atom type classification for oxygen that would be useful in biochemical investigations. 

Define the following terms (a) United force field, (b) All atom force field For theoretical calculations, limits on computational time forces researchers to decide which systems need all atom force fields to be accurately modeled and which ones can be modeled using united force fields. Assuming you are a researcher who only has enough computational power to use all atom force fields on three of the six following systems, which of them would be most accurately modeled using united force fields and why  

Phospholipids located in a membrane, phospholipids (as second messengers) in the cytosol, sphingomyelin, folded protein structures, reactive sites of enzymes, nucleic acids in the zinc finger of the chromosome. Wliat are tire assumptions and constraints for each of these molecular modeling systems (a) Force field methods, (b) Semi-empirical method, (c) Ab initio method. 

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