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Molecular mechanical potential functions and their application to study molecular systems

Identifieur interne : 004916 ( Main/Exploration ); précédent : 004915; suivant : 004917

Molecular mechanical potential functions and their application to study molecular systems

Auteurs : Wendy D. Cornell [États-Unis] ; Allison E. Howard [États-Unis] ; Peter Kollman [États-Unis]

Source :

RBID : ISTEX:9E61FF242E5A8B98981CCF521B13107608699A64

English descriptors

Abstract

Abstract: In this review, we attempt to describe the critical issues involved in the parameterization and use of molecular mechanical force fields. This review contains six sections: an introduction to the issues; a description of the technical issues in molecular mechanics; comparisons and evaluations of force fields; improving and extending force fields; combining force fields with experimental data; and conformational searching.

Url:
DOI: 10.1016/0959-440X(91)90062-X


Affiliations:


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Le document en format XML

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<term>Alanyl dipeptide</term>
<term>Aliphatic amines</term>
<term>Amber force field</term>
<term>Amino acids</term>
<term>Annealing</term>
<term>Aromatic molecules</term>
<term>Atomic charges</term>
<term>Atomic dipoles</term>
<term>Atomic point charges</term>
<term>Benzene</term>
<term>Best agreement</term>
<term>Best correlation</term>
<term>Biol</term>
<term>Biomol struct</term>
<term>Biopolymers</term>
<term>Bond lengths</term>
<term>Bond rotations</term>
<term>Carbonyl groups</term>
<term>Carlo</term>
<term>Cartesian derivatives</term>
<term>Charge flux</term>
<term>Charge transfer</term>
<term>Charmm</term>
<term>Charmm force field</term>
<term>Chem</term>
<term>Chem phys</term>
<term>Comp chem</term>
<term>Comput</term>
<term>Comput cbem</term>
<term>Comput chem</term>
<term>Computational time</term>
<term>Computationally</term>
<term>Conformation</term>
<term>Conformational</term>
<term>Conformational analysis</term>
<term>Conformational sampling</term>
<term>Constant dielectric</term>
<term>Constraint</term>
<term>Coulombic interaction</term>
<term>Crambin</term>
<term>Crystal structure</term>
<term>Crystalline hydrates</term>
<term>Crystallographic data</term>
<term>Crystallographic structure</term>
<term>Cutoff</term>
<term>Derivative</term>
<term>Dielectric</term>
<term>Diffraction data</term>
<term>Dihedral space</term>
<term>Dinur</term>
<term>Dynamics</term>
<term>Ecepp potentials</term>
<term>Electron density</term>
<term>Electronegativity</term>
<term>Electronegativity gradient</term>
<term>Electronegativity parameters</term>
<term>Electrostatic force</term>
<term>Electrostatic interactions</term>
<term>Empirical force fields</term>
<term>Energy conservation</term>
<term>Energy functions</term>
<term>Energy hypersurface</term>
<term>Energy refinement</term>
<term>Energy surface</term>
<term>Equilibrium geometry</term>
<term>Experimental data</term>
<term>Force constants</term>
<term>Force field</term>
<term>Force field calculations</term>
<term>Force fields</term>
<term>Fourier series</term>
<term>Free energy</term>
<term>Functional form</term>
<term>Functional forms</term>
<term>Good agreement</term>
<term>Higher correlations</term>
<term>Higher multipoles</term>
<term>Initial geometry</term>
<term>Initio</term>
<term>Initio calculations</term>
<term>Initio energy surfaces</term>
<term>Initio quantum mechanics</term>
<term>Initio values</term>
<term>Intermolecular terms</term>
<term>Internal coordinates</term>
<term>Ionic molecules</term>
<term>Kollman</term>
<term>Lattice</term>
<term>Lattice constants</term>
<term>Lattice energies</term>
<term>Liquid benzene</term>
<term>Liquid properties</term>
<term>Liquid water</term>
<term>Local minima</term>
<term>Lone pairs</term>
<term>Lowenergy conformations</term>
<term>Many groups</term>
<term>Mndo</term>
<term>Mndo wave functions</term>
<term>Model systems</term>
<term>Modeling metalloproteins</term>
<term>Molecular dynamics</term>
<term>Molecular dynamics simulations</term>
<term>Molecular mechanics</term>
<term>Molecule</term>
<term>Monopole model</term>
<term>Monte carlo methods</term>
<term>Monte carlo simulations</term>
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<term>Nucleic acids</term>
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<term>Parameter</term>
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<term>Partial equalization</term>
<term>Peptide</term>
<term>Periodic boundary conditions</term>
<term>Phys</term>
<term>Phys chem</term>
<term>Planar dimers</term>
<term>Point dipoles</term>
<term>Polarizability</term>
<term>Polypeptide</term>
<term>Potential energy</term>
<term>Potential energy surface</term>
<term>Potential functions</term>
<term>Potential functions cornell</term>
<term>Protein crambin</term>
<term>Protein structure</term>
<term>Protein tendamistat</term>
<term>Quality structure</term>
<term>Quantum mechanics</term>
<term>Radial distribution function</term>
<term>Reaction rates</term>
<term>Refinement</term>
<term>Relative bond asymmetry</term>
<term>Second derivatives</term>
<term>Second moments</term>
<term>Second peak</term>
<term>Simpler representations</term>
<term>Simulating protein</term>
<term>Simulation</term>
<term>Small model systems</term>
<term>Small molecules</term>
<term>Solution conformation</term>
<term>Solvated protein</term>
<term>Solvation</term>
<term>Solvent effects</term>
<term>Spectroscopic force fields</term>
<term>Structural biology</term>
<term>Structural data</term>
<term>Structural transitions</term>
<term>Structure factors</term>
<term>Such methods</term>
<term>Technical issues</term>
<term>Theoryand simulation</term>
<term>Thermal motion</term>
<term>Thermodynamic properties</term>
<term>Torsion</term>
<term>Torsional</term>
<term>Torsional parameters</term>
<term>Total interaction energy</term>
<term>Transition state</term>
<term>Various approaches</term>
<term>Vibrational frequencies</term>
<term>Waals parameters</term>
<term>Water model</term>
<term>Water models</term>
<term>Wave function</term>
<term>Weiner</term>
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<div type="abstract" xml:lang="en">Abstract: In this review, we attempt to describe the critical issues involved in the parameterization and use of molecular mechanical force fields. This review contains six sections: an introduction to the issues; a description of the technical issues in molecular mechanics; comparisons and evaluations of force fields; improving and extending force fields; combining force fields with experimental data; and conformational searching.</div>
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