force field of biological system - 科学院理论物理研 .pptVIP

Force Field of Biological System Why do we need force field? 1. Force Fields Classical Newtonian Dynamics Electrons are in the ground state Force fields are approximate Nonbonded force fields for biological systems are effective pair potentials No Explicit term for hydrogen bonding 2. Commonly used force fields Amber: Assisted Model Building with Energy Refinement CHARMM: Chemistry at HARvard Macromolecular Mechanics OPLS-AA: Optimized Potentials for Liquid Simulations- All Atom GROMOS: GROningen MOlecular Simulation 3. Functional forms 4. Differences for bonded interactions AMBER: CHARMM: + OPLS-AA: GROMOS: 5. Differences for nonbonded interactions 6. How to construct a force field? Experimental: vibrational spectra; heats of vaporization; densities; solvation free energies; microwave, electron, or X-ray diffraction structure; and relative conformational energies and barrier heights. QM: vibrational spectra; minimum energy geometries; dipole moments; conformational energies and barrier heights; electrostatic potentials; and dimerization energies AMBER84: Polar hydrogens + united atoms ( hydrogens bonded to carbon) AMBER86: All- atom model Based on experimental with gas phase simulation AMBER94: Aimed to better perform Condensed phase simulations Partial charges: Dependency on environments: RESP Dependency on conformations: fit simultaneously with multiple configurations 6. Comparison of force field in realization THANK YOU * 中国科学院理论物理研究所 张小虎 研究生院《分子建模与模拟导论》课堂 2009年10月21日 References H. J. C. Berendsen, et al, Gromacs User Manual version 4.0 A. D. MacKerell, Jr. , et al, Comparison of Protein Force Fields for Molecular Dynamics Simulations“ A. D. Mackerell, Jr. , et al, Empirical Force Fields for Biological Macromolecules: Overview and Issues“ J. W. Ponder, et al, FORCE FIELDS FOR PROTEIN SIMULATIONS