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   force field parameter sets

Tinker


6. Force Field Parameter Sets

The TINKER package is distributed with several force field parameter sets, implementing a selection of widely used literature force fields as well as the TINKER force field currently under construction in the Ponder lab. We try to exactly reproduce the intent of the original authors of our distributed, third-party force fields. In all cases the parameter sets have been validated against literature reports, results provided by the original developers, or calculations made with the authentic programs. With the few exceptions noted below, TINKER calculations can be treated as authentic results from the genuine force fields. A brief description of each parameter set, including some still in preparation and not distributed with the current version, is provided below with lead references:

AMBER.PRM

AMBER-95 parameters for proteins. Note that with their "Cornell" force field, the Kollman group has devised separate, fully independent partial charge values for each of the N- and Cterminal residues. At present, the terminal residue charges for TINKER's version maintain the correct formal charge, but redistributed somewhat from the Kollman group values. The file reproduces the authentic parm94 set; torsional parameter changes for parm96 are noted in that section of the file.

W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman, A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules, J. Am. Chem. Soc. , 117, 5179-5197 (1995) [PARM94]

P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot and A. Pohorille, The Development/ Application of a 'Minimalist' Organic/Biochemical Molecular Mechanic Force Field using a Combination of ab Initio Calculations and Experimental Data, in Computer Simulation of Biomolecular Systems , W. F. van Gunsteren, P. K. Weiner, A. J. Wilkinson, eds., Volume 3, 83-96 (1997) [PARM96]

G. Moyna, H. J. Williams, R. J. Nachman and A. I. Scott, Conformation in Solution and Dynamics of a Structurally Constrained Linear Insect Kinin Pentapeptide Analogue, Biopolymers, 49, 403-413 (1999) [AIB charges]

W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy Perturbation Studies, J. Am. Chem. Soc. , 116, 4363-4366 (1994) [alkali metal ions]

J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J. Phys. Chem. , 94, 8021-8024, 1990 [alkaline earth Ions, radii adapted for AMBER combining rule]

Current parameter values are available from the AMBER site in Peter Kollman's lab at UCSF, http://www.amber.ucsf.edu/amber/amber.html/

AMBERN.PRM

AMBER-95 parameters for nucleic acids that correspond to the "Cornell" force field as published by the Kollman group.

W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman, A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules, J. Am. Chem. Soc. , 117, 5179-5197 (1995)

Current parameter values are available from the AMBER site in Peter Kollman's lab at UCSF, http://www.amber.ucsf.edu/amber/amber.html/

CHARMM.PRM

CHARMM22 parameters for proteins. Most of the nucleic acid, lipid and small model compound parameters are not yet implemented. We plan to provide the CHARMM27 nucleic acid parameters in due course as a separate parameter file.

N. Foloppe and A. D. MacKerell, Jr., All-Atom Empirical Force Field for Nucleic Acids: 1)

Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data, J. Comput. Chem. , 21, 86-104 (2000) [CHARMM27]

N. Banavali and A. D. MacKerell, Jr., All-Atom Empirical Force Field for Nucleic Acids: 2)

Application to Molecular Dynamics Simulations of DNA and RNA in Solution, J. Comput. Chem., 21, 105-120 (2000)

A. D. MacKerrell, Jr., et al. , All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B , 102, 3586- 3616 (1998) [CHARMM22]

A. D. MacKerell, Jr., J. Wiorkeiwicz-Kuczera and M. Karplus, An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids, J. Am. Chem. Soc. , 117, 11946-11975 (1995)

S. E. Feller, D. Yin, R. W. Pastor and A. D. MacKerell, Jr., Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies, Biophysical Journal , 73, 2269-2279 (1997) [alkenes]

R. H. Stote and M. Karplus, Zinc Binding in Proteins and Solution - A Simple but Accurate Nonbonded Representation, Proteins, 23, 12-31 (1995) [zinc ion]

Current parameter values are available from the CHARMM parameter site in Alex MacKerell's lab at UMBC, http://www.pharmacy.ab.umd.edu/~alex/

EMR.PRM

Reduced EMR model adapted for flexible sidechains. Only a few amino acid residue types have been implemented.

R. V. Pappu, W. J. Schneller and D. L. Weaver, Electrostatic Multipole Representation of a Polypeptide Chain: An Algorithm for Simulation of Polypeptide Properties, J. Comput. Chem., 17, 1033-1055 (1996)

ENCAD.PRM

ENCAD parameters for proteins and nucleic acids. ( in preparation )

M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Potential Energy Function and Parameters for Simulations of the Molecular Dynamics of Protein and Nucleic Acids in Solution, Comp. Phys. Commun. , 91, 215-231 (1995)

M. Levitt, M. Hirshberg, R. Sharon, K. E. Laidig and V. Daggett, Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Protein and Nucleic Acids in Solution, J. Phys. Chem. B , 101, 5051-5061 (1997) [F3C water]

HOCH.PRM

Simple NMR-NOE force field of Hoch and Stern.

J. C. Hoch and A. S. Stern, A Method for Determining Overall Protein Fold from NMR Distance Restraints, J. Biomol. NMR , 2, 535-543 (1992)

MERCK.PRM

Preliminary MMFF vdw parameters using buffered 14/7 function.

T. A. Halgren, Representation of van der Waals (vdW) Interactions in Molecular Mechanics Force Fields: Potential Form, Combination Rules, and vdW Parameters, J. Am. Chem. Soc. , 114, 7827-7843 (1992)

MM2.PRM

Full MM2(1991) parameters including π-systems. The anomeric and electronegativity correction terms included in some later versions of MM2 are not implemented.

N. L. Allinger, Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms, J. Am. Chem. Soc. , 99, 8127-8134 (1977)

J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, The MMP2 Calculational Method, J. Comput. Chem. , 8, 581-603 (1987)

J. C. Tai and N. L. Allinger, Molecular Mechanics Calculations on Conjugated Nitrogen- Containing Heterocycles, J. Am. Chem. Soc. , 110, 2050-2055 (1988)

J. C. Tai, J.-H. Lii and N. L. Allinger, A Molecular Mechanics (MM2) Study of Furan, Thiophene, and Related Compounds, J. Comput. Chem. , 10, 635- 647 (1989)

N. L. Allinger, R. A. Kok and M. R. Imam, Hydrogen Bonding in MM2, J. Comput. Chem. , 9, 591-595 (1988)

L. Norskov-Lauritsen and N. L. Allinger, A Molecular Mechanics Treatment of the Anomeric Effect, J. Comput. Chem. , 5, 326-335 (1984)

All parameters distributed with TINKER are from the "MM2 (1991) Parameter Set", as provided by N. L. Allinger, University of Georgia

MM3.PRM

Full MM3(2000) parameters including pi-systems. The directional hydrogen bonding term and electronegativity bond length corrections are implemented, but the anomeric and Bohlmann correction terms are not implemented.

N. L. Allinger, Y. H. Yuh and J.-H. Lii, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1, J. Am. Chem. Soc. , 111, 8551-8566 (1989)

J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2. Vibrational Frequencies and Thermodynamics, J. Am. Chem. Soc. , 111, 8566-8575 (1989)

J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 3. The van der Waals' Potentials and Crystal Data for Aliphatic and Aromatic Hydrocarbons, J. Am. Chem. Soc. , 111, 8576- 8582 (1989)

N. L. Allinger, H. J. Geise, W. Pyckhout, L. A. Paquette and J. C. Gallucci, Structures of Norbornane and Dodecahedrane by Molecular Mechanics Calculations (MM3), X-ray Crystallography, and Electron Diffraction, J. Am. Chem. Soc. , 111, 1106-1114 (1989) [stretch-torsion cross term]

N. L. Allinger, F. Li and L. Yan, Molecular Mechanics. The MM3 Force Field for Alkenes, J. Comput. Chem. , 11, 848-867 (1990)

N. L. Allinger, F. Li, L. Yan and J. C. Tai, Molecular Mechanics (MM3) Calculations on Conjugated Hydrocarbons, J. Comput. Chem. , 11, 868-895 (1990)

J.-H. Lii and N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. I, J. Phys. Org. Chem. , 7, 591-609 (1994)

J.-H. Lii and N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. II, J. Comput. Chem. , 19, 1001-1016 (1998)

All parameters distributed with TINKER are from the "MM3 (2000) Parameter Set", as provided by N. L. Allinger, University of Georgia, August 2000

MM3PRO.PRM

Protein-only version of the MM3 parameters.

J.-H. Lii and N. L. Allinger, The MM3 Force Field for Amides, Polypeptides and Proteins, J. Comput. Chem. , 12, 186-199 (1991)

MMFFPRO.PRM

Protein-only version of the MMFF94 parameters. ( in preparation )

T. A. Halgren, Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94, J. Comput. Chem. , 17, 490-519, 1996

OPLS.PRM

Complete OPLS-UA with united-atom parameters for proteins and many classes of organic molecules. Explicit hydrogens on polar atoms and aromatic carbons.

W. L. Jorgensen and J. Tirado-Rives, The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin, J. Am. Chem. Soc. , 110, 1657- 1666 (1988) [peptide and proteins]

W. L. Jorgensen and D. L. Severance, Aromatic-Aromatic Interactions: Free Energy Profiles for the Benzene Dimer in Water, Chloroform, and Liquid Benzene, J. Am. Chem. Soc. , 112, 4768-4774 (1990) [aromatic hydrogens]

S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr. and P. Weiner, A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins, J. Am. Chem. Soc. , 106, 765-784 (1984) [united- atom "AMBER/OPLS" local geometry] S. J. Weiner, P. A. Kollman, D. T. Nguyen and D. A. Case, An All Atom Force Field for Simulations of Proteins and Nucleic Acids, J. Comput. Chem. , 7, 230-252 (1986) [all-atom "AMBER/OPLS" local geometry]

L. X. Dang and B. M. Pettitt, Simple Intramolecular Model Potentials for Water, J. Phys. Chem., 91, 3349-3354 (1987) [flexible TIP3P and SPC water]

W. L. Jorgensen, J. D. Madura and C. J. Swenson, Optimized Intermolecular Potential Functions for Liquid Hydrocarbons, J. Am. Chem. Soc. , 106, 6638-6646 (1984) [hydrocarbons]

W. L. Jorgensen, E. R. Laird, T. B. Nguyen and J. Tirado-Rives, Monte Carlo Simulations of Pure Liquid Substituted Benzenes with OPLS Potential Functions, J. Comput. Chem. , 14, 206-215 (1993) [substituted benzenes]

E. M. Duffy, P. J. Kowalczyk and W. L. Jorgensen, Do Denaturants Interact with Aromatic Hydrocarbons in Water?, J. Am. Chem. Soc. , 115, 9271-9275 (1993) [benzene, naphthalene, urea, guanidinium, tetramethyl ammonium]

W. L. Jorgensen and C. J. Swenson, Optimized Intermolecular Potential Functions for Amides and Peptides. Structure and Properties of Liquid Amides, J. Am. Chem. Soc. , 106, 765-784 (1984) [amides]

W. L. Jorgensen, J. M. Briggs and M. L. Contreras, Relative Partition Coefficients for Organic Solutes form Fluid Simulations, J. Phys. Chem. , 94, 1683- 1686 (1990) [chloroform, pyridine, pyrazine, pyrimidine]

J. M. Briggs, T. B. Nguyen and W. L. Jorgensen, Monte Carlo Simulations of Liquid Acetic Acid and Methyl Acetate with the OPLS Potential Functions, J. Phys. Chem. , 95, 3315-3322 (1991) [acetic acid, methyl acetate]

H. Liu, F. Muller-Plathe and W. F. van Gunsteren, A Force Field for Liquid Dimethyl Sulfoxide and Physical Properties of Liquid Dimethyl Sulfoxide Calculated Using Molecular Dynamics Simulation, J. Am. Chem. Soc. , 117, 4363- 4366 (1995) [dimethyl sulfoxide]

J. Gao, X. Xia and T. F. George, Importance of Bimolecular Interactions in Developing Empirical Potential Functions for Liquid Ammonia, J. Phys. Chem. , 97, 9241-9246 (1993) [ammonia]

J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J. Phys. Chem. , 94, 8021-8024 (1990) [metal ions]

W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy Perturbation Studies, J. Am. Chem. Soc. , 116, 4363-4366 (1994) [alkali metal ions]

J. Chandrasekhar, D. C. Spellmeyer and W. L. Jorgensen, Energy Component Analysis for Dilute Aqueous Solutions of Li+, Na+, F-, and Cl- Ions, J. Am. Chem. Soc. , 106, 903-910 (1984) [halide ions]

Most parameters distributed with TINKER are from "OPLS and OPLS-AA Parameters for Organic Molecules, Ions, and Nucleic Acids" as provided by W. L. Jorgensen, Yale University, October 1997

OPLSAA.PRM

OPLS-AA with all-atom parameters for proteins and many general classes of organic molecules.

W. L. Jorgensen, D. S. Maxwell and J. Tirado-Rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc. , 118, 11225- 11236 (1996)

W. L. Jorgensen and N. A. McDonald, Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyridine and Diazenes, THEOCHEM-J. Mol. Struct. , 424, 145-155 (1998)

N. A. McDonald and W. L. Jorgensen, Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyrrole, Furan, Diazoles, and Oxazoles, J. Phys. Chem. B, 102, 8049-8059 (1998)

All parameters distributed with TINKER are from "OPLS and OPLS-AA Parameters for Organic Molecules, Ions, and Nucleic Acids" as provided by W. L. Jorgensen, Yale University, October 1997

SMOOTH.PRM

Version of OPLS-UA for use with potential smoothing. Largely adapted largely from standard OPLS-UA parameters with modifications to the vdw and improper torsion terms.

R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization, J. Phys, Chem. B , 102, 9725-9742 (1998) [smoothing modifications]

SMOOTHAA.PRM

Version of OPLS-AA for use with potential smoothing. Largely adapted largely from standard OPLS-AA parameters with modifications to the vdw and improper torsion terms.

R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization, J. Phys, Chem. B , 102, 9725-9742 (1998) [smoothing modifications]

TINKER.PRM

Protein-only parameters for the TINKER force field with multipole values of Dudek and Ponder. The current file contains all the multipole values, but the local geometry and vdw terms are still under development.

WATER.PRM

The current TINKER water parameters for a polarizable multipole electrostatics model. This model is equal or better to the best available water models for many bulk and cluster properties.

Y. Kong and J. W. Ponder, Calculation of the Reaction Field Due to Off-Center Point Multipoles, J. Chem. Phys. , 107, 481-492 (1997)

The parameters distributed with TINKER are modified values based on the work of Pengyu Ren starting from the Ph.D. thesis of Yong Kong, "Multipole Electrostatic Methods for Protein Modeling with Reaction Field Treatment", Biochemistry & Molecular Biophysics, Washington University, St. Louis, August, 1997




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