CHARMM energy calculation

In another example of differences in complexity, the bondstretching energy in CHARMM is calculated with a harmonic oscillator function. MM3 solves the problem described by French, Tran and Perez in this book for MM2 s cubic stretching function by using a quartic function for bond stretching. Additional complexity in MM3 is described in Ref. 12. 

The AMBER (271, 272) and CHARMM (179) nonbonded terms are used as scoring function in several docking programs. As mentioned above (Sections.1.1), protein terms are usually precalculated on a rectangular grid to speed up the energy calculation compared to traditional atom-by-atom evaluations (273). Distance-dependent dielectric constants are... 

Initial structures were refined against both the experimental restraints and the CHARMM energy using a novel simulated annealing protocol to define the torsion angle solutions to within an error of about 5°. Forty refined structures were used to obtain an average structure which was then further refined. A dielectric constant of 1 was used in the calculations. 

Nicklaus MC. Conformational energies calculated by the molecular mechanics program CHARMm. J Comput Chem 1997 18 1056-1060. 

In the following, the VALBOND-TRANS force field is parametrized for model octahedral complexes of Ir, with the aim to best capture relative energies calculated from DPT for different diastereomers. The (re-)parametrization of VALBOND-TRANS is important for successful use in further atomistic simulations. The fitting procedure can be conveniently carried out by using a recent combination of CHARMM and the I-NoLLS fitting environment [79, 80]. This parameter optimization environment can carry out interactive nonlinear least-square fittings to determine model parameters for a wide variety of applications. 

Molecular mechanics, which uses classical mechanics and predetermined force fields to explain the behavior of atoms in molecules. They consider atoms as spheres and bonds as springs. They use an algebraic classical mechanics equation for the energy calculation. The constants in the equation are obtained from experimental data or other calculations and are stored in a data library. The combination of constants and equations is called a force field. These calculations are simple and can be done with many software programs such as AMBER [49] and CHARMM [50]. There are lot of force fields available and some of the popular force fields are UFF [51], MM4 [52], andMMFF94 [53]. 

Bernhard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. CHARMM A program for macro-molecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4(2) 187-217, 1983. 

Brooks, B.R. Bruccoleri, R.E. Olafson, B.D. States, D.J. Swaminathan, S. Karpins, M. CHARMM A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187-217, 1983. 

---