Lennard-Jones potential energy proteins

In both equations, d is the separation between the atoms. The Lennard-Jones potential is simpler and computationally less demanding and is therefore favored for models of macromolecules such as proteins and DNA. The Buckingham function more closely resembles the energy relationship and is preferred when higher accuracy is required. The latter function is available in MOMEC and we will concentrate on this. 

We have developed such a force field, named SPEEDY (Simplified Parameters for Energy Evaluation and DYnamics). SPEEDY uses the QPACK protein model and residue interaction potentials.- The terms of the potential function are analogous to those used in molecular mechanics calculations. Since the backbone virtual dihedral and bond angles are dependent on the complicated geometry of the polypeptide backbone, these terms are not represented independently. Residue interactions are represented by Lennard-Jones type functions scaled by their... 

All protein atoms except hydrogens bonded to carbon were explicitly represented. Positions of polar hydrogens were calculated on the basis of coordinates of the heavier atoms (5) and standard geometric constraints (14). The non-bonded energy for the interaction of the water molecule and the protein was calculated as a sum of electrostatic and 6-12 Lennard-Jones attractive and repulsive contributions for the three atoms of the water molecule and all atoms of the protein within 6 X of the water oxygen s center. Empirical parameters were used for the 6-12 potentials (15,16,17), partial atomic charges were values obtained with molecular orbital calculations (1 ) for hydrogen-bonded interactions modified 6-12 parameters were used (18). 

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