Automation of AMOEBA polarizable force field parameterization for small molecules

Theoretical Chemistry Accounts

Volumn 131, Issue 3, 2012, Pages 1-11

  Wu, Johnny C ^a   Chattree, Gaurav ^a   Ren, Pengyu ^a  

^a The University of Texas at Austin   (United States)

Author keywords

AMOEBA; Atomic typer; Molecular dynamics; Polarizable force field; Poltype; Small molecule modeling

Indexed keywords

EID: 84862791277     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-012-1138-6     Document Type: Article

References (64)

1. Buckingham AD (1967) Permanent and induced molecular moments and long-range intermolecular forces. Adv Chem Phys 12: 107-142.
2. Jensen L, Astrand PO, Osted A, Kongsted J, Mikkelsen KV (2002) Polarizability of molecular clusters as calculated by a dipole interaction model. J Chem Phys 116(10): 4001-4010.
3. Gresh N, Cisneros GA, Darden TA, Piquemal JP (2007) Anisotropic, polarizable molecular mechanics studies of inter- and intramoecular interactions and ligand-macromolecule complexes. A bottom-up strategy. J Chem Theory Comput 3(6): 1960-1986.
4. Piquemal JP, Williams-Hubbard B, Fey N, Deeth RJ, Gresh N, Giessner-Prettre C (2003) Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. J Comput Chem 24(16): 1963-1970.
5. Rick SW, Stuart SJ, Berne BJ (1994) Dynamical fluctuating charge force-fields: application to liquid water. J Chem Phys 101(7): 6141-6156.
6. Xie W, Orozco M, Truhlar DG, Gao J (2009) X-Pol potential: an electronic structure-based force field for molecular dynamics simulation of a solvated protein in water. J Chem Theory Comput 5(3): 459-467.
7. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angewandte Chemie-Int Ed 48(7): 1198-1229.
8. Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23(16): 1623-1641.
9. Cieplak P, Dupradeau FY, Duan Y, Wang JM (2009) Polarization effects in molecular mechanical force fields. J Phys Condens Matter 21(33): 333102.
10. Lopes PEM, Roux B, MacKerell AD (2009) Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications. Theor Chem Acc 124(1-2): 11-28.
11. Klimovich PV, Mobley DL (2010) Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J Comput-Aided Mol Des 24(4): 307-316.
12. Bauer BA, Warren GL, Patel S (2009) Incorporating phase-dependent polarizability in nonadditive electrostatic models for molecular dynamics simulations of the aqueous liquid-vapor interface. J Chem Theory Comput 5(2): 359-373.
13. Cezard C, Bouvier B, Brenner V, Defranceschi M, Millie P, Soudan JM, Dognon JP (2004) Theoretical investigation of small alkali cation-molecule: a model potential approach. J Phys Chem B 108(4): 1497-1506.
14. Jiao D, King C, Grossfield A, Darden TA, Ren PY (2006) Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B 110(37): 18553-18559.
15. Yu HB, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, MacKerell AD, Roux B (2010) Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field. J Chem Theory Comput 6(3): 774-786.
16. Wu JC, Piquemal JP, Chaudret R, Reinhardt P, Ren PY (2010) Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. J Chem Theory Comput 6(7): 2059-2070.
17. Jiao D, Golubkov PA, Darden TA, Ren P (2008) Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci USA 105(17): 6290-6295.
18. Jiao D, Zhang JJ, Duke RE, Li GH, Schnieders MJ, Ren PY (2009) Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem 30(11): 1701-1711.
19. Shi Y, Jiao DA, Schnieders MJ, Ren PY (2009) Trypsin-ligand binding free energy calculation with AMOEBA. EMBC 2009 Ann Int Conf IEEE Eng Med Biol Soc 1-20: 2328-2331. http://dx. crossref. org/10. 1109%2FIEMBS. 2009. 5335108.
20. Xie WS, Pu JZ, MacKerell AD, Gao JL (2007) Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J Chem Theory Comput 3(6): 1878-1889.
21. Wang JM, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graphics Model 25(2): 247-260.
22. Moriarty NW, Grosse-Kunstleve RW, Adams PD (2009) Electronic ligand builder and optimization workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr Sect D Biol Crystallogr 65: 1074-1080.
23. Ren PY, Ponder JW (2002) Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J Comput Chem 23(16): 1497-1506.
24. Ren PY, Ponder JW (2003) Polarizable atomic multipole water model for molecular mechanics simulation. J Phys Chem B 107(24): 5933-5947.
25. Ponder JW, Wu CJ, Ren PY, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GNI, Johnson ME, Head-Gordon T (2010) Current Status of the AMOEBA polarizable force field. J Phys Chem B 114(8): 2549-2564.
26. Allinger NL, Yuh YH, Lii JH (1989) Molecular mechanics: the MM3 force-field for hydrocarbons. 1. J Am Chem Soc 111(23): 8551-8566.
27. Wilson EB, Decius JC, Cross PC (1955) Molecular vibrations: the theory of infrared and raman vibrational spectra. McGraw-Hill, New York.
28. Halgren TA (1992) Representation of vanderwaals (Vdw) interactions in molecular mechanics force-fields: potential form, combination rules, and Vdw parameters. J Am Chem Soc 114(20): 7827-7843.
29. Thole BT (1981) Molecular polarizabilities calculated with a modified dipole interaction. Chem Phys 59(3): 341-350.
30. Burnham CJ, Li JC, Xantheas SS, Leslie M (1999) The parametrization of a Thole-type all-atom polarizable water model from first principles and its application to the study of water clusters (n = 2-21) and the phonon spectrum of ice Ih. J Chem Phys 110(9): 4566-4581.
31. Weininger D (1988) Smiles, a chemical language and information-system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 28(1): 31-36.
32. Morgan HL (1965) The generation of a unique machine description for chemical structures-a technique developed at chemical abstracts service. J Chem Document 5(2): 107-113.
33. Stone AJ, Alderton M (1985) Distributed multipole analysis: methods and applications. Mol Phys 56(5): 1047-1064.
34. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, M. Ishida TN, Y. Honda, O. Kitao HN, Vreven T, J. A. Montgomery J, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, A. D. Daniels, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09. Revision D. 1 edn. Gaussian, Inc., Wallingford CT.
35. Stone AJ (2005) Distributed multipole analysis: stability for large basis sets. J Chem Theory Comput 1(6): 1128-1132.
36. Shi Y, Wu CJ, Ponder JW, Ren PY (2011) Multipole electrostatics in hydration free energy calculations. J Comput Chem 32(5): 967-977.
37. Singh J, Thornton JM (1992) Atlas of protein side-chain interactions, vol I & II. IRL press, Oxford.
38. Thornton JM (2009) http://www. ebi. ac. uk/thornton-srv/databases/sidechains/.
39. Abraham MH, Whiting GS, Fuchs R, Chambers EJ (1990) Thermodynamics of solute transfer from water to hexadecane. J Chem Soc Perkin Trans 2(2): 291-300.
40. Chambers CC, Hawkins GD, Cramer CJ, Truhlar DG (1996) Model for aqueous solvation based on class IV atomic charges and first solvation shell effects. J Phys Chem 100(40): 16385-16398.
41. Berka K, Laskowski R, Riley KE, Hobza P, Vondrasek J (2009) Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures. J Chem Theory Comput 5(4): 982-992.
42. Tsuzuki S, Honda K, Uchimaru T, Mikami M (2005) Ab initio calculations of structures and interaction energies of toluene dimers including CCSD(T) level electron correlation correction. J Chem Phys 122(14): 144323.
43. Sinnokrot MO, Sherrill CD (2004) Highly accurate coupled cluster potential energy curves for the benzene dimer: Sandwich, T-shaped, and parallel-displaced configurations. J Phys Chem A 108(46): 10200-10207.
44. Hobza P, Sponer J (1999) Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. Chem Rev 99(11): 3247-3276.
45. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105(28): 6474-6487.
46. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong GM, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang JM, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16): 1999-2012.
47. Rapcewicz K, Ashcroft NW (1991) Fluctuation attraction in condensed matter: a nonlocal functional-approach. Phys Rev B 44(8): 4032-4035.
48. Andersson Y, Hult E, Apell P, Langreth DC, Lundqvist BI (1998) Density-functional account of van der Waals forces between parallel surfaces. Solid State Commun 106(5): 235-238.
49. Ahmed HU, Blakeley MP, Cianci M, Cruickshank DWJ, Hubbard JA, Helliwell JR (2007) The determination of protonation states in proteins. Acta Crystallog Sect D Biol Crystallogr 63: 906-922.
50. Fenn TD, Schnieders MJ, Brunger AT, Pande VS (2010) Polarizable atomic multipole X-Ray refinement: hydration geometry and application to macromolecules. Biophys J 98(12): 2984-2992.
51. Faver JC, Benson ML, He XA, Roberts BP, Wang B, Marshall MS, Kennedy MR, Sherrill CD, Merz KM (2011) Formal estimation of errors in computed absolute interaction energies of protein-ligand complexes. J Chem Theory Comput 7(3): 790-797.
52. Bennett CH (1976) Efficient estimation of free-energy differences from monte-carlo data. J Comput Phys 22(2): 245-268.
53. Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR (1984) Molecular-dynamics with coupling to an external bath. J Chem Phys 81(8): 3684-3690.
54. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh ewald method. J Chem Phys 103(19): 8577-8593.
55. Darden T, York D, Pedersen L (1993) Particle mesh ewald: an N. Log(N) method for ewald sums in large systems. J Chem Phys 98(12): 10089-10092.
56. Sagui C, Darden TA (1999) Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Annu Rev Biophys Biomol Struct 28: 155-179.
57. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA (2009) Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations. J Chem Theory Comput 5(2): 350-358.
58. Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25(9): 1157-1174.
59. Jakalian A, Bush BL, Jack DB, Bayly CI (2000) Fast, efficient generation of high-quality atomic Charges. AM1-BCC model: I. Method. J Comput Chem 21(2): 132-146.
60. Schmid R, Miah AM, Sapunov VN (2000) A new table of the thermodynamic quantities of ionic hydration: values and some applications (enthalpy-entropy compensation and Born radii). Phys Chem Chem Phys 2(1): 97-102.
61. Krishnan CV, Friedman HL (1970) Solvation enthalpies of various ions in water and heavy water. J Phys Chem 74(11): 2356.
62. Tissandier MD, Cowen KA, Feng WY, Gundlach E, Cohen MH, Earhart AD, Tuttle TR, Coe JV (1998) The proton's absolute aqueous enthalpy and Gibbs free energy of solvation from cluster ion solvation data (vol 102A, pg 7791, 1998). J Phys Chem A 102(46): 9308.
63. Grossfield A, Ren PY, Ponder JW (2003) Ion solvation thermodynamics from simulation with a polarizable force field. J Am Chem Soc 125(50): 15671-15682.
64. Kelly CP, Cramer CJ, Truhlar DG (2006) Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton. J Phys Chem B 110(32): 16066-16081.