Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

We have developed a polarizable force field for peptides, using all-atom OPLS (OPLS-AA) nonelectrostatic terms and electrostatics based on a fluctuating charge model and fit to ab initio calculations of polarization responses. We discuss the fitting procedure, and specific techniques we have developed that are necessary in order to obtain an accurate, stable model. Our model is comparable to the best existing molecular mechanics force fields in reproducing quantum-chemical peptide energetics. It also accurately reproduces many-body effects in many cases. We believe that straightforward extensions of our linear-response electrostatic model will significantly improve the accuracy for those cases that the present model does not adequately address.

[1]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[2]  Richard A. Friesner,et al.  Constructing ab initio force fields for molecular dynamics simulations , 1998 .

[3]  Peter A. Kollman,et al.  Ion solvation in polarizable water: molecular dynamics simulations , 1991 .

[4]  C. J. Casewit,et al.  Application of a universal force field to organic molecules , 1992 .

[5]  R. Parr.  Density-functional theory of atoms and molecules , 1989 .

[6]  R. Parr,et al.  Electronegativity: The density functional viewpoint , 1978 .

[7]  Steven J. Stuart,et al.  Dynamical fluctuating charge force fields: Application to liquid water , 1994 .

[8]  T. Halgren.  Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[9]  Thomas A. Halgren,et al.  Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 , 1996, J. Comput. Chem..

[10]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[11]  Wilfried J. Mortier,et al.  Electronegativity-equalization method for the calculation of atomic charges in molecules , 1986 .

[12]  R. T. Sanderson,et al.  An Interpretation of Bond Lengths and a Classification of Bonds. , 1951, Science.

[13]  B. Honig,et al.  New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects , 1996 .

[14]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

[15]  T. Halgren,et al.  Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules , 1996 .

[16]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[17]  N. L. Allinger,et al.  Molecular Mechanics (MM3). Calculations of Furan, Vinyl Ethers, and Related Compounds , 1993 .

[18]  Thomas A. Halgren,et al.  Merck molecular force field. IV. conformational energies and geometries for MMFF94 , 1996 .

[19]  Ming-Jing Hwang,et al.  Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules , 1994 .

[20]  Ming-Jing Hwang,et al.  Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules , 1994, J. Comput. Chem..

[21]  Richard A. Friesner,et al.  Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields , 1997 .

[22]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[23]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[24]  Johann Gasteiger,et al.  Electronegativity equalization: application and parametrization , 1985 .

[25]  Ronald M. Levy,et al.  SOLVATION FREE ENERGIES OF SMALL AMIDES AND AMINES FROM MOLECULAR DYNAMICS/FREE ENERGY PERTURBATION SIMULATIONS USING PAIRWISE ADDITIVE AND MANY-BODY POLARIZABLE POTENTIALS , 1995 .

[26]  Darrin M. York,et al.  A chemical potential equalization method for molecular simulations , 1996 .

[27]  T. Halgren.  Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions , 1996 .

[28]  L. E. Chirlian,et al.  Atomic charges derived from electrostatic potentials: A detailed study , 1987 .

[29]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[30]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[31]  Dan N. Bernardo,et al.  An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields , 1994 .

[32]  W. Goddard,et al.  Charge equilibration for molecular dynamics simulations , 1991 .

[33]  R. T. Sanderson.  Chemical Bonds and Bond Energy , 1976 .