Force fields, Molecular Mechanics AMBER

We have pursued a plug-and-play strategy with two different energy functions, a molecular mechanics AMBER force field [131,132] and a simplified energy function, along with two different sampling techniques, evolutionary programming [91] and Monte Carlo simulations [118,119,127,128]. 

Standard molecular mechanics (MM) methods (e.g. the popular force fields developed for AMBER, CHARMM and GROMOS decribed in Section 2 above) provide a good description of protein structure and dynamics, but cannot be used to model chemical reactions. This limitation is due their simple functional forms (e.g. harmonic terms for bond stretching) and inability to model changes in electronic polarization (because of the invariant point partial atomic charge used by these molecular mechanics methods to represent electrostatic interactions). 

A step forward along the route to the correct modelling of the spectroscopy and photochemical reactivity of photoreactive proteins is represented by the implementation of a Quantum Mechanics/Molecular Mechanics (QM/MM) computational strategy based on a suitable QM part coupled with a protein force field such as AMBER [34] (or CHARMM [35]). Very recently a CASPT2//CASSCF/AMBER method for rhodopsin has been implemented in our laboratory [36,37] within the QM/MM hnk-atom scheme [38]. Special care has been taken in the parametrization of the protonated Schiff base linkage region that describes the dehcate border region between the MM (the protein)... 

Force field-based scoring functions are based on the nonbonded terms of a classical molecular mechanics force field (e.g.. Amber and CHARMm). A Lennard-Jones potential describes van der Waals interactions, whereas the Coulomb energy describes the electrostatic components of the interactions. The nonbonded interaction energy takes the following form ... 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

TlypcrC hcm oilers four molecular mechanics force fields MM+, AMBER, BIO+, and OPES (sec References on page 106). To run a molecular mechanics calciilaLion. yon miisi lirsi choose a force Eeld. The following sections discuss considerations in choosing a force field. 

Hach molecular mechanics method has its own functional form MM+. AMBER, OPL.S, and BIO+. The functional form describes the an alytic form of each of th e term s in th e poteri tial. For exam pie, MM+h as both a quadratic and a cubic stretch term in th e poten tial whereas AMBER, OPES, and BIO+ have only c nadratic stretch term s, I h e functional form is referred to here as the force field. For exam pie, th e fun ction al form of a qu adratic stretch with force constant K, and equilibrium distance i q is ... 

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

AMBER (assisted model building with energy refinement) a molecular mechanics force field... 

This discussion focuses on the individual components of a typical molecular mechanics force field. It illustrates the mathematical functions used, why those functions are chosen, and the circumstances under which the functions become poor approximations. Part 2 of this book. Theory and Methods, includes details on the implementation of the MM-t, AMBER, BlO-t, and OPES force fields in HyperChem. 

Quantum mechanical calculations generally have only one carbon atom type, compared with the many types of carbon atoms associated with a molecular mechanics force field like AMBER. Therefore, the number of quantum mechanics parameters needed for all possible molecules is much smaller. In principle, very accurate quantum mechanical calculations need no parameters at all, except fundamental constants such as the speed of light, etc. 

Theoretical models include those based on classical (Newtonian) mechanical methods—force field methods known as molecular mechanical methods. These include MM2, MM3, Amber, Sybyl, UFF, and others described in the following paragraphs. These methods are based on Hook s law describing the parabolic potential for the stretching of a chemical bond, van der Waal s interactions, electrostatics, and other forces described more fully below. The combination assembled into the force field is parameterized based on fitting to experimental data. One can treat 1500-2500 atom systems by molecular mechanical methods. Only this method is treated in detail in this text. Other theoretical models are based on quantum mechanical methods. These include ... 

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