Energy with CHARMM

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 derivatives of these energies with respect to the coordinates of the QM and MM atoms are easily formulated. The remaining term Emm in Eq. (17-18) is composed from two-body electrostatic and LJ interactions and can be computed by utilizing the parameter set of potential field such as Amber, Charmm, or OPLS. 

The reimaging of atoms that move outside of the primary simulation cell, a common feature of bulk simulations with CHARMM, was not used in the present work. It was found to produce a decreasing and abnormally fluctuating system energy. This behavior may have resulted from the short cutoff being employed, a possibility that shall be examined. 

In this paper we develop a new method for finding the three-dimensional space that surrounds a substrate/ligand. This space, which is the chemical equivalent of the receptor, is represented as a protein structure, referred herein as a "pseudo-receptor". A variety of computational tools are used to create the pseudo-receptor. A molecular mechanics and dynamics program, CHARMm(l), is used to calculate the energy and conformational features of the pseudo-receptor. The program QUANTA(l) is used to define the preliminary protein sequence, secondary structure, graphically examine molecular interactions, interface with CHARMm, and model amino-acid mutations in the protein sequence. 

Nevertheless, the geometiy-based hybrid orbital strength functions turned out to be useful to capture the angular parts of force fields. Therefore, VALBOND is used in conjunction with a conventional force field such as CHARMM, where the typical harmonic bending terms are replaced with a new parametrization. In fact, VALBOND was developed together with CHARMM [59]. The additional energy term is of the form... 

The kind of energy terms, their functional form, and how carefully (number, quality, and kind of reference data) the parameters were derived determine the quality of a force field. Accurate force fields exist for organic molecules (e.g., MM2, MM3), but more approximate force fields (e.g., with fixed bond distances) optimized for computational speed rather than accuracy [e.g., AMBER (assisted model building with energy refinement), CHARMM (chemistry at Harvard molecular mechanics), GROMOS (Groningen molecular simulation)] are the only practical choice for the treatment of large biomolecules. The type of molecular system to be smdied determines the choice of the force field. 

Of the biomolecular force fields, AMBER [21] is considered to be transferable, whereas academic CHARMM [20] is not transferable. Considering the simplistic form of the potential energy functions used in these force fields, the extent of transferability should be considered to be minimal, as has been shown recently [52]. As stated above, the user should perform suitable tests on any novel compounds to ensure that the force field is treating the systems of interest with sufficient accuracy. 

This term is essential to obtain the correct geometry, because there is no Pauli repulsion between quantum and classical atoms. The molecular mechanics energy tenn, E , is calculated with the standard potential energy term from CHARMM [48], AMBER [49], or GROMOS [50], for example. 

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