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Volumn 8, Issue 9, 2012, Pages 3207-3216

Polarizable mean-field model of water for biological simulations with AMBER and CHARMM force fields

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EID: 84866177485     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300011h     Document Type: Article
Times cited : (100)

References (52)
  • 1
    • 0036285985 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M. Molecular dynamics simulations of biomolecules Acc. Chem. Res. 2002, 35, 321-323
    • (2002) Acc. Chem. Res. , vol.35 , pp. 321-323
    • Karplus, M.1
  • 2
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M.; McCammon, J. A. Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 2002, 9, 646-652
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 5
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 8
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins - Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen, W. L.; Tirado-Rives, J. The OPLS potential functions for proteins-energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 1988, 110, 1657-1666
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 9
    • 0029912748 scopus 로고    scopus 로고
    • Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 10
    • 0442311067 scopus 로고    scopus 로고
    • Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry
    • Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A. Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry J. Phys. Chem. A 2004, 108, 621-627
    • (2004) J. Phys. Chem. A , vol.108 , pp. 621-627
    • Kaminski, G.A.1    Stern, H.A.2    Berne, B.J.3    Friesner, R.A.4
  • 11
    • 4043057278 scopus 로고    scopus 로고
    • CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
    • Patel, S.; Mackerell, A. D., Jr.; Brooks, C. L., III. CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model J. Comput. Chem. 2004, 25, 1504-1514
    • (2004) J. Comput. Chem. , vol.25 , pp. 1504-1514
    • Patel, S.1    Mackerell Jr., A.D.2    Brooks III, C.L.3
  • 12
    • 30344482264 scopus 로고    scopus 로고
    • A polarizable model of water for molecular dynamics simulations of biomolecules
    • Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. A polarizable model of water for molecular dynamics simulations of biomolecules Chem. Phys. Lett. 2006, 418, 245-249
    • (2006) Chem. Phys. Lett. , vol.418 , pp. 245-249
    • Lamoureux, G.1    Harder, E.2    Vorobyov, I.V.3    Roux, B.4    MacKerell, A.D.5
  • 13
    • 0037899660 scopus 로고    scopus 로고
    • Polarizable atomic multipole water model for molecular mechanics simulation
    • Ren, P. Y.; Ponder, J. W. Polarizable atomic multipole water model for molecular mechanics simulation J. Phys. Chem. B 2003, 107, 5933-5947
    • (2003) J. Phys. Chem. B , vol.107 , pp. 5933-5947
    • Ren, P.Y.1    Ponder, J.W.2
  • 15
    • 84961983456 scopus 로고    scopus 로고
    • Accounting for electronic polarization in non-polarizable force fields
    • Leontyev, I. V.; Stuchebrukhov, A. A. Accounting for electronic polarization in non-polarizable force fields Phys. Chem. Chem. Phys. 2011, 13, 2613-2626
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 2613-2626
    • Leontyev, I.V.1    Stuchebrukhov, A.A.2
  • 16
    • 84961978300 scopus 로고    scopus 로고
    • Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules
    • Leontyev, I. V.; Stuchebrukhov, A. A. Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules J. Chem. Theory Comput. 2010, 6, 1498-1508
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1498-1508
    • Leontyev, I.V.1    Stuchebrukhov, A.A.2
  • 17
    • 79551625777 scopus 로고    scopus 로고
    • Electronic Polarizability and the Effective Pair Potentials of Water
    • Leontyev, I. V.; Stuchebrukhov, A. A. Electronic Polarizability and the Effective Pair Potentials of Water J. Chem. Theory Comput. 2010, 6, 3153-3161
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 3153-3161
    • Leontyev, I.V.1    Stuchebrukhov, A.A.2
  • 18
    • 0242384207 scopus 로고    scopus 로고
    • Continuum level treatment of electronic polarization in the framework of molecular simulations of solvation effects
    • Leontyev, I. V.; Vener, M. V.; Rostov, I. V.; Basilevsky, M. V.; Newton, M. D. Continuum level treatment of electronic polarization in the framework of molecular simulations of solvation effects J. Chem. Phys. 2003, 119, 8024-8037
    • (2003) J. Chem. Phys. , vol.119 , pp. 8024-8037
    • Leontyev, I.V.1    Vener, M.V.2    Rostov, I.V.3    Basilevsky, M.V.4    Newton, M.D.5
  • 19
    • 61449183750 scopus 로고    scopus 로고
    • Electronic continuum model for molecular dynamics simulations
    • Leontyev, I. V.; Stuchebrukhov, A. A. Electronic continuum model for molecular dynamics simulations J. Chem. Phys. 2009, 130, 085102
    • (2009) J. Chem. Phys. , vol.130 , pp. 085102
    • Leontyev, I.V.1    Stuchebrukhov, A.A.2
  • 20
    • 0142057630 scopus 로고    scopus 로고
    • Structural, electronic, and bonding properties of liquid water from first principles
    • Silvestrelli, P. L.; Parrinello, M. Structural, electronic, and bonding properties of liquid water from first principles J. Chem. Phys. 1999, 111, 3572-3580
    • (1999) J. Chem. Phys. , vol.111 , pp. 3572-3580
    • Silvestrelli, P.L.1    Parrinello, M.2
  • 21
    • 34547268706 scopus 로고    scopus 로고
    • Dipolar correlations and the dielectric permittivity of water
    • Sharma, M.; Resta, R.; Car, R. Dipolar correlations and the dielectric permittivity of water Phys. Rev. Lett. 2007, 98, 247401
    • (2007) Phys. Rev. Lett. , vol.98 , pp. 247401
    • Sharma, M.1    Resta, R.2    Car, R.3
  • 22
    • 33645934660 scopus 로고
    • Fluids of Polarizable Hard-Spheres with Dipoles and Tetrahedral Quadrupoles - Integral-Equation Results with Application to Liquid Water
    • Carnie, S. L.; Patey, G. N. Fluids of Polarizable Hard-Spheres with Dipoles and Tetrahedral Quadrupoles-Integral-Equation Results with Application to Liquid Water Mol. Phys. 1982, 47, 1129-1151
    • (1982) Mol. Phys. , vol.47 , pp. 1129-1151
    • Carnie, S.L.1    Patey, G.N.2
  • 23
    • 25844474073 scopus 로고    scopus 로고
    • Accounting for polarization in molecular simulation
    • Yu, H. B.; van Gunsteren, W. F. Accounting for polarization in molecular simulation Comput. Phys. Commun. 2005, 172, 69-85
    • (2005) Comput. Phys. Commun. , vol.172 , pp. 69-85
    • Yu, H.B.1    Van Gunsteren, W.F.2
  • 25
    • 0001196127 scopus 로고
    • Effective Pair Potentials and the Properties of Water
    • Watanabe, K.; Klein, M. L. Effective Pair Potentials and the Properties of Water Chem. Phys. 1989, 131, 157-167
    • (1989) Chem. Phys. , vol.131 , pp. 157-167
    • Watanabe, K.1    Klein, M.L.2
  • 26
    • 0003397206 scopus 로고
    • 2 nd ed. Elsevier Sci. Pub. Co. Amsterdam, section: "The internal field for non-polar dielectrics".
    • Bottcher, C. J. F. Theory of Electric Polarization, 2 nd ed.; Elsevier Sci. Pub. Co.: Amsterdam, 1973; Vol. I, section: "The internal field for non-polar dielectrics".
    • (1973) Theory of Electric Polarization , vol.1
    • Bottcher, C.J.F.1
  • 28
    • 0242321249 scopus 로고    scopus 로고
    • Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular-continuum approach
    • Vener, M. V.; Leontyev, I. V.; Basilevsky, M. V. Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular-continuum approach J. Chem. Phys. 2003, 119, 8038-8046
    • (2003) J. Chem. Phys. , vol.119 , pp. 8038-8046
    • Vener, M.V.1    Leontyev, I.V.2    Basilevsky, M.V.3
  • 29
    • 0010884753 scopus 로고
    • On the Theory of Oxidation-Reduction Reactions Involving Electron Transfer. i
    • Marcus, R. A. On the Theory of Oxidation-Reduction Reactions Involving Electron Transfer. I J. Chem. Phys. 1956, 24, 966-978
    • (1956) J. Chem. Phys. , vol.24 , pp. 966-978
    • Marcus, R.A.1
  • 30
    • 0009869207 scopus 로고
    • Electrostatic Free Energy and Other Properties of States Having Nonequilibrium Polarization 1
    • Marcus, R. A. Electrostatic Free Energy and Other Properties of States Having Nonequilibrium Polarization 1 J. Chem. Phys. 1956, 24, 979-989
    • (1956) J. Chem. Phys. , vol.24 , pp. 979-989
    • Marcus, R.A.1
  • 31
    • 84863696122 scopus 로고    scopus 로고
    • Accurate description of aqueous carbonate ions: An effective polarization model verified by neutron scattering
    • Mason, P. E.; Wernersson, E.; Jungwirth, P. Accurate description of aqueous carbonate ions: An effective polarization model verified by neutron scattering J. Phys. Chem. B 2012, 116, 8145-8153
    • (2012) J. Phys. Chem. B , vol.116 , pp. 8145-8153
    • Mason, P.E.1    Wernersson, E.2    Jungwirth, P.3
  • 32
    • 84864746574 scopus 로고    scopus 로고
    • Ions at hydrophobic aqueous interfaces: Molecular dynamics with effective polarization
    • Vazdar, M.; Pluhařová, E.; Mason, P. E.; Vácha, R.; Jungwirth, P. Ions at hydrophobic aqueous interfaces: Molecular dynamics with effective polarization J. Phys. Chem. Lett. 2012, 3, 2087-291
    • (2012) J. Phys. Chem. Lett. , vol.3 , pp. 2087-291
    • Vazdar, M.1    Pluhařová, E.2    Mason, P.E.3    Vácha, R.4    Jungwirth, P.5
  • 33
    • 84863652661 scopus 로고    scopus 로고
    • Solvation and ion-pairing properties of the aqueous sulfate anion: Explicit versus effective electronic polarization
    • Pegado, L.; Marsalek, O.; Jungwirth, P.; Wernersson, E. Solvation and ion-pairing properties of the aqueous sulfate anion: Explicit versus effective electronic polarization Phys. Chem. Chem. Phys. 2012, 14, 10248-10257
    • (2012) Phys. Chem. Chem. Phys. , vol.14 , pp. 10248-10257
    • Pegado, L.1    Marsalek, O.2    Jungwirth, P.3    Wernersson, E.4
  • 36
    • 0036569841 scopus 로고    scopus 로고
    • What can classical simulators learn from ab initio simulations?
    • Delle Site, L.; Lynden-Bell, R. M.; Alavi, A. What can classical simulators learn from ab initio simulations? J. Mol. Liq. 2002, 98-99, 79-86
    • (2002) J. Mol. Liq. , vol.9899 , pp. 79-86
    • Delle Site, L.1    Lynden-Bell, R.M.2    Alavi, A.3
  • 37
    • 0342394897 scopus 로고
    • The dielectric polarization of polar liquids
    • Kirkwood, J. G. The dielectric polarization of polar liquids J. Chem. Phys. 1939, 7, 911-919
    • (1939) J. Chem. Phys. , vol.7 , pp. 911-919
    • Kirkwood, J.G.1
  • 38
    • 0343791148 scopus 로고
    • Electric moments of molecules in liquids
    • Onsager, L. Electric moments of molecules in liquids J. Am. Chem. Soc. 1936, 58, 1486-1493
    • (1936) J. Am. Chem. Soc. , vol.58 , pp. 1486-1493
    • Onsager, L.1
  • 39
    • 84961980477 scopus 로고    scopus 로고
    • Quantum Mechanical Continuum Solvation Models
    • Tomasi, J.; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models Chem. Rev. 2005, 105, 2999-3094
    • (2005) Chem. Rev. , vol.105 , pp. 2999-3094
    • Tomasi, J.1    Mennucci, B.2    Cammi, R.3
  • 40
    • 36448999850 scopus 로고
    • Dynamical fluctuating charge force fields: Application to liquid water
    • Rick, S. W.; Stuart, S. J.; Berne, B. J. Dynamical fluctuating charge force fields: Application to liquid water J. Chem. Phys. 1994, 101, 6141-6156
    • (1994) J. Chem. Phys. , vol.101 , pp. 6141-6156
    • Rick, S.W.1    Stuart, S.J.2    Berne, B.J.3
  • 41
    • 0041878923 scopus 로고    scopus 로고
    • Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
    • Lamoureux, G.; Roux, B. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm J. Chem. Phys. 2003, 119, 3025-3039
    • (2003) J. Chem. Phys. , vol.119 , pp. 3025-3039
    • Lamoureux, G.1    Roux, B.2
  • 42
    • 70350406220 scopus 로고    scopus 로고
    • Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D
    • Kunz, A. P. E.; van Gunsteren, W. F. Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D J. Phys. Chem. A 2009, 113, 11570-11579
    • (2009) J. Phys. Chem. A , vol.113 , pp. 11570-11579
    • Kunz, A.P.E.1    Van Gunsteren, W.F.2
  • 44
    • 0003998388 scopus 로고    scopus 로고
    • Internet Version 2010, 90 ed. CRC Press/Taylor and Francis: Boca Raton, FL.
    • Lide, D. R. CRC Handbook of Chemistry and Physics, Internet Version 2010, 90 ed.; CRC Press/Taylor and Francis: Boca Raton, FL, 2010.
    • (2010) CRC Handbook of Chemistry and Physics
    • Lide, D.R.1
  • 45
    • 37049095962 scopus 로고
    • Pressure and Temperature-Dependence of Self-Diffusion in Water
    • Krynicki, K.; Green, C. D.; Sawyer, D. W. Pressure and Temperature-Dependence of Self-Diffusion in Water Faraday Discuss. 1978, 66, 199-208
    • (1978) Faraday Discuss. , vol.66 , pp. 199-208
    • Krynicki, K.1    Green, C.D.2    Sawyer, D.W.3
  • 46
    • 0033984826 scopus 로고    scopus 로고
    • A new table of the thermodynamic quantities of ionic hydration: Values and some applications (enthalpy-entropy compensation and Born radii)
    • Schmid, R.; Miah, A. M.; Sapunov, V. N. A new table of the thermodynamic quantities of ionic hydration: values and some applications (enthalpy-entropy compensation and Born radii) Phys. Chem. Chem. Phys. 2000, 2, 97-102
    • (2000) Phys. Chem. Chem. Phys. , vol.2 , pp. 97-102
    • Schmid, R.1    Miah, A.M.2    Sapunov, V.N.3
  • 47
    • 36449006356 scopus 로고
    • Molecular dynamics simulation of a polymer chain in solution
    • Dunweg, B.; Kremer, K. Molecular dynamics simulation of a polymer chain in solution J. Chem. Phys. 1993, 99, 6983-6997
    • (1993) J. Chem. Phys. , vol.99 , pp. 6983-6997
    • Dunweg, B.1    Kremer, K.2
  • 49
    • 49449085241 scopus 로고    scopus 로고
    • Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
    • Joung, I. S.; Cheatham, T. E. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations J. Phys. Chem. B 2008, 112, 9020-9041
    • (2008) J. Phys. Chem. B , vol.112 , pp. 9020-9041
    • Joung, I.S.1    Cheatham, T.E.2
  • 51
    • 1242314254 scopus 로고    scopus 로고
    • Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome c Oxidase
    • Popovic, D. M.; Stuchebrukhov, A. A. Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome c Oxidase J. Am. Chem. Soc. 2004, 126, 1858-1871
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 1858-1871
    • Popovic, D.M.1    Stuchebrukhov, A.A.2


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