Skip to main content
SpringerLink
Log in

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Polarizable force fields are emerging as a more accurate alternative to additive force fields in terms of modeling and simulations of a variety of chemicals including biomolecules. Explicit treatment of induced polarization in charged species such as phosphates and sulfates offers the potential for achieving an improved atomistic understanding of the physical forces driving their interactions with their environments. To help achieve this, in this study we present balanced Drude polarizable force field parameters for molecular ions including phosphates, sulfates, sulfamates, and oxides. Better balance was primarily achieved in the relative values of minimum interaction energies and distances of the anionic model compounds with water at the Drude and quantum mechanical (QM) model chemistries. Parametrization involved reoptimizing available parameters as well as extending the force field to new molecules with the goal of achieving self-consistency with respect to the Lennard-Jones and electrostatic parameters targeting QM and experimental hydration free energies. The resulting force field parameters achieve consistent treatment across the studied anions, facilitating more balanced simulations of biomolecules and small organic molecules in the context of the classical Drude polarizable force field.

Graphical abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Whitford PC, Blanchard SC, Cate JH, Sanbonmatsu KY (2013) Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol 9(3):e1003003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Dror RO, Pan AC, Arlow DH, Borhani DW, Maragakis P, Shan Y et al (2011) Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci U S A 108(32):13118–13123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP et al (2010) Atomic-level characterization of the structural dynamics of proteins. Science. 330(6002):341–346

    Article  CAS  PubMed  Google Scholar 

  4. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature. 267(5612):585–590

    Article  CAS  PubMed  Google Scholar 

  5. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM et al (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179–5197

    Article  CAS  Google Scholar 

  6. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102(18):3586–3616

    Article  CAS  PubMed  Google Scholar 

  7. MacKerell AD, Brooks B, Brooks CL, Nilsson L, Roux B, Won Y et al (2002) CHARMM: the energy function and its parameterization. Encyclopedia of Computational Chemistry. Wiley

  8. Guvench O, Hatcher E, Venable RM, Pastor RW, MacKerell AD (2009) CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses. J Chem Theory Comput 5(9):2353–2370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. MacKerell Jr AD, Banavali N, Foloppe N (2000) Development and current status of the CHARMM force field for nucleic acids. Biopolymers. 56(4):257–265

    Article  CAS  PubMed  Google Scholar 

  10. Pastor RW, Mackerell Jr AD (2011) Development of the CHARMM force field for lipids. J Phys Chem Lett 2(13):1526–1532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. 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

    Article  CAS  Google Scholar 

  12. Damm W, Frontera A, Tirado-Rives J, Jorgensen WL (1997) OPLS all-atom force field for carbohydrates. J Comput Chem 18(16):1955–1970

    Article  CAS  Google Scholar 

  13. Soares TA, Hunenberger PH, Kastenholz MA, Krautler V, Lenz T, Lins RD et al (2005) An improved nucleic acid parameter set for the GROMOS force field. J Comput Chem 26(7):725–737

    Article  CAS  PubMed  Google Scholar 

  14. Pol-Fachin L, Rusu VH, Verli H, Lins RD (2012) GROMOS 53A6GLYC, an improved GROMOS force field for hexopyranose-based carbohydrates. J Chem Theory Comput 8(11):4681–4690

    Article  CAS  PubMed  Google Scholar 

  15. Jungwirth P, Tobias DJ (2001) Molecular structure of salt solutions: a new view of the interface with implications for heterogeneous atmospheric chemistry. J Phys Chem B 105(43):10468–10472

    Article  CAS  Google Scholar 

  16. Chang T-M, Dang LX (2006) Recent advances in molecular simulations of ion solvation at liquid interfaces. Chem Rev 106(4):1305–1322

    Article  CAS  PubMed  Google Scholar 

  17. Jungwirth P, Tobias DJ (2006) Specific ion effects at the air/water interface. Chem Rev 106(4):1259–1281

    Article  CAS  PubMed  Google Scholar 

  18. Warshel A, Kato M, Pisliakov AV (2007) Polarizable force fields: history, test cases, and prospects. J Chem Theory Comput 3(6):2034–2045

    Article  CAS  PubMed  Google Scholar 

  19. Freddolino PL, Harrison CB, Liu Y, Schulten K (2010) Challenges in protein folding simulations: timescale, representation, and analysis. Nat Phys 6(10):751–758

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Lopes PEM, Roux B, MacKerell AD (2009) Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications. Theor Chem Accounts 124(1):11–28

    Article  CAS  Google Scholar 

  21. Zhu X, Lopes PEM, MacKerell Jr AD (2012) Recent developments and applications of the CHARMM force fields. WIREs Comput Mol Sci 2(1):167–185

    Article  CAS  Google Scholar 

  22. Lemkul JA, Savelyev A, MacKerell Jr AD (2014) Induced polarization influences the fundamental forces in DNA base flipping. J Phys Chem Lett 5(12):2077–2083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lemkul JA, MacKerell Jr AD (2018) Polarizable force field for RNA based on the classical drude oscillator. J Comput Chem 39(32):2624–2646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Huang J, MacKerell Jr AD (2014) Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. Biophys J 107(4):991–997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Lin FY, MacKerell Jr AD (2019) Improved modeling of cation-pi and anion-ring interactions using the Drude polarizable empirical force field for proteins. J Comput Chem

  26. Lemkul JA (2019) Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes. Nucleic Acids Res

  27. Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M et al (2011) Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies. J Phys Chem B 115(12):3100–3111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Wang J, Cieplak P, Cai Q, Hsieh MJ, Wang J, Duan Y et al (2012) Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes. J Phys Chem B 116(28):7999–8008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Shi Y, Xia Z, Zhang J, Best R, Wu C, Ponder JW et al (2013) The polarizable atomic multipole-based AMOEBA force field for proteins. J Chem Theory Comput 9(9):4046–4063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Patel S, Brooks CL (2004) III CHARMM fluctuating charge force fields for proteins: I Paramaterization and application to bulk organic liquid simulations. J Comput Chem 25(1):1–16

    Article  CAS  PubMed  Google Scholar 

  31. Wang ZX, Zhang W, Wu C, Lei H, Cieplak P, Duan Y (2006) Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J Comput Chem 27(6):781–790

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Westheimer FH (1987) Why nature chose phosphates. Science. 235(4793):1173–1178

    Article  CAS  PubMed  Google Scholar 

  33. Kehoe JW, Bertozzi CR (2000) Tyrosine sulfation: a modulator of extracellular protein-protein interactions. Chem Biol 7(3):R57–R61

    Article  CAS  PubMed  Google Scholar 

  34. Winum J-Y, Scozzafava A, Montero J-L, Supuran CT (2005) Sulfamates and their therapeutic potential. Med Res Rev 25(2):186–228

    Article  CAS  PubMed  Google Scholar 

  35. Rami M, Dubois L, Parvathaneni N-K, Alterio V, van Kuijk SJA, Monti SM et al (2013) Hypoxia-targeting carbonic anhydrase IX inhibitors by a new series of nitroimidazole-sulfonamides/sulfamides/sulfamates. J Med Chem 56(21):8512–8520

    Article  CAS  PubMed  Google Scholar 

  36. Halgren TA, Damm W (2001) Polarizable force fields. Curr Opin Struct Biol 11(2):236–242

    Article  CAS  PubMed  Google Scholar 

  37. Lemkul JA, Huang J, Roux B, MacKerell Jr AD (2016) An empirical polarizable force field based on the classical Drude oscillator model: development history and recent applications. Chem Rev 116(9):4983–5013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Cieplak P, Dupradeau FY, Duan Y, Wang J (2009) Polarization effects in molecular mechanical force fields. J Phys Condens Matter 21(33):333102

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66:27–85

    Article  CAS  PubMed  Google Scholar 

  40. Baker CM (2015) Polarizable force fields for molecular dynamics simulations of biomolecules. WIREs Comput Mol Sci 5(2):241–254

    Article  CAS  Google Scholar 

  41. Lin FY, MacKerell Jr AD (2018) Polarizable empirical force field for halogen-containing compounds based on the classical Drude oscillator. J Chem Theory Comput 14(2):1083–1098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Lin FY, Lopes PEM, Harder E, Roux B, MacKerell Jr AD (2018) Polarizable force field for molecular ions based on the classical Drude oscillator. J Chem Inf Model 58(5):993–1004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Small MC, Aytenfisu AH, Lin F-Y, He X, MacKerell AD (2017) Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des:1–15

  44. Lemkul JA, MacKerell Jr AD (2017) Polarizable force field for DNA based on the classical Drude oscillator: II. Microsecond molecular dynamics simulations of duplex DNA. J Chem Theory Comput 13(5):2072–2085

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lemkul JA, Lakkaraju SK, MacKerell Jr AD (2016) Characterization of Mg(2+) distributions around RNA in solution. ACS Omega 1(4):680–688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Yang M, Aytenfisu AH, MacKerell Jr AD (2018) Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field. Carbohydr Res 457:41–50

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Aytenfisu AH, Yang M, MacKerell Jr AD (2018) CHARMM Drude polarizable force field for glycosidic linkages involving pyranoses and furanoses. J Chem Theory Comput 14(6):3132–3143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Lamoureux G, Roux B (2003) Modeling induced polarization with Drude oscillators: theory and molecular dynamics simulation algorithm. J Chem Phys 119(6):3025–3039

    Article  CAS  Google Scholar 

  49. Jiang W, Hardy DJ, Phillips JC, Mackerell AD, Schulten K, Roux B (2011) High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. J Phys Chem Lett 2(2):87–92

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Lemkul JA, Roux B, van der Spoel D, MacKerell Jr AD (2015) Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J Comput Chem 36(19):1473–1479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP et al (2013) OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation. J Chem Theory Comput 9(1):461–469

    Article  CAS  PubMed  Google Scholar 

  52. Huang J, Lemkul JA, Eastman PK, MacKerell Jr AD (2018) Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: implementation, validation, and benchmarks. J Comput Chem 39(21):1682–1689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Metz S, Kästner J, Sokol AA, Keal TW, Sherwood P (2014) ChemShell—a modular software package for QM/MM simulations. WIREs Comput Mol Sci 4(2):101–110

    Article  CAS  Google Scholar 

  54. Lu Y, Farrow MR, Fayon P, Logsdail AJ, Sokol AA, Catlow CRA et al (2019) Open-source, python-based redevelopment of the ChemShell multiscale QM/MM environment. J Chem Theory Comput 15(2):1317–1328

    Article  PubMed  CAS  Google Scholar 

  55. Sherwood P, de Vries AH, Guest MF, Schreckenbach G, Catlow CRA, French SA et al (2003) QUASI: a general purpose implementation of the QM/MM approach and its application to problems in catalysis. J Mol Struct THEOCHEM 632(1):1–28

    Article  CAS  Google Scholar 

  56. Savelyev A, MacKerell Jr AD (2014) All-atom polarizable force field for DNA based on the classical drude oscillator model. J Comput Chem 10:1652–1664

    Google Scholar 

  57. Li H, Chowdhary J, Huang L, He X, MacKerell Jr AD, Roux B (2017) Drude polarizable force field for molecular dynamics simulations of saturated and unsaturated zwitterionic lipids. J Chem Theory Comput 13(9):4535–4552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell Jr AD, Roux B (2013) A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B 117(31):9142–9160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Villa F, MacKerell Jr AD, Roux B, Simonson T (2018) Classical Drude polarizable force field model for methyl phosphate and its interactions with mg(2). J Phys Chem A 122(29):6147–6155

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Parrish RM, Burns LA, Smith DGA, Simmonett AC, DePrince 3rd AE, Hohenstein EG et al (2017) Psi4 1.1: an open-source electronic structure program emphasizing automation, advanced libraries, and interoperability. J Chem Theory Comput 13(7):3185–3197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR et al (2003) Gaussian 03. Revision B.04 ed. Gaussian, Inc., Pittsburgh

    Google Scholar 

  62. Lamoureux G, Harder E, Vorobyov I, Roux B, MacKerell Jr AD (2006) A polarizable model of water for molecular dynamics simulations of biomolecules. Chem Phys Lett 418:245–249

    Article  CAS  Google Scholar 

  63. Boys SF, Bernardi F (1970) The calculation of Small molecular interaction by the differences of Seperate Total energies. Some procedures with reduced errors. Mol Phys 19:553–566

    Article  CAS  Google Scholar 

  64. Ransil B (1961) Studies in molecular structure IV. Potential curve for the interaction of two helium atoms in single-configuration LCAO MO SCF approximation. J Chem Phys 34:2109

    Article  CAS  Google Scholar 

  65. Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell Jr AD (2005) Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. J Chem Theory Comput 1(1):153–168

    Article  PubMed  CAS  Google Scholar 

  66. Kumar A, Yoluk O, MacKerell Jr AD (2019) FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules. J Comput Chem

  67. Vanommeslaeghe K, Yang M, MacKerell Jr AD (2015) Robustness in the fitting of molecular mechanics parameters. J Comput Chem 36(14):1083–1101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Kollman PA (1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 93:2395–2417

    Article  CAS  Google Scholar 

  69. Brooks BR, Brooks III CL, MacKerell Jr AD, Nilsson L, Petrella RJ, Roux B et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545–1614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Deng Y, Roux B (2004) Hydration of amino acid side chains: nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules. J Phys Chem B 108:16567–16576

    Article  CAS  Google Scholar 

  71. Harder E, Roux B (2008) On the origin of the electrostatic potential difference at a liquid-vacuum interface. J Chem Phys 129(23):234706

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  72. Lamoureux G, Roux B (2006) Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. J Phys Chem B 110(7):3308–3322

    Article  CAS  PubMed  Google Scholar 

  73. Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM et al (2010) Simulating monovalent and divalent ions in aqueous solution using a Drude polarizable force field. J Chem Theory Comput 6(3):774–786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Baker CM, Lopes PE, Zhu X, Roux B, MacKerell Jr AD (2010) Accurate calculation of hydration free energies using pair-specific Lennard-Jones parameters in the CHARMM Drude polarizable force field. J Chem Theory Comput 6(4):1181–1198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. PyMOL: The PyMOL molecular graphics system, version 2.0 Schrödinger, LLC

  76. Baker CM, Mackerell Jr AD (2010) Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers. J Mol Model 16(3):567–576

    Article  CAS  PubMed  Google Scholar 

  77. Schropp B, Tavan P (2008) The polarizability of point-polarizable water models: density functional theory/molecular mechanics results. J Phys Chem B 112(19):6233–6240

    Article  CAS  PubMed  Google Scholar 

  78. Kamitakahara A, Hsu C-L, Pranata J (1995) Reexamination of the conformations of dimethyl phosphate anion in water. J Mol Struct THEOCHEM 334(1):29–35

    Article  CAS  Google Scholar 

  79. Ibargüen C, Manrique-Moreno M, Hadad CZ, David J, Restrepo A (2013) Microsolvation of dimethylphosphate: a molecular model for the interaction of cell membranes with water. Phys Chem Chem Phys 15(9):3203–3211

    Article  PubMed  CAS  Google Scholar 

  80. Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C et al (2010) Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 114(23):7830–7843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. George P, Witonsky RJ, Trachtman M, Wu C, Dorwart W, Richman L et al (1970) “Squiggle-H2O”. An enquiry into the importance of solvation effects in phosphate ester and anhydride reactions. Biochim Biophys Acta 223(1):1–15

    Article  CAS  PubMed  Google Scholar 

  82. Steinbrecher T, Latzer J, Case DA (2012) Revised AMBER parameters for bioorganic phosphates. J Chem Theory Comput 8(11):4405–4412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Marcus Y (1991) Thermodynamics of solvation of ions. Part 5.—Gibbs free energy of hydration at 298.15 K. J Chem Soc Faraday Trans 87(18):2995–2999

    Article  CAS  Google Scholar 

  84. Li J, Zhu T, Hawkins GD, Winget P, Liotard DA, Cramer CJ et al (1999) Extension of the platform of applicability of the SM5.42R universal solvation model. Theor Chem Accounts 103(1):9–63

    Article  CAS  Google Scholar 

  85. 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

    Article  CAS  PubMed  Google Scholar 

  86. Kelly CP, Cramer CJ, Truhlar DG (2005) SM6: a density functional theory continuum solvation model for calculating aqueous solvation free energies of neutrals, ions, and solute−water clusters. J Chem Theory Comput 1(6):1133–1152

    Article  CAS  PubMed  Google Scholar 

  87. Park S-J, Lee J, Patel DS, Ma H, Lee HS, Jo S et al (2017) Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank. Bioinformatics

  88. Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA et al (2016) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force Field. J Chem Theory Comput 12(1):405–413

    Article  CAS  PubMed  Google Scholar 

  89. Patel DS, He X, MacKerell Jr AD (2015) Polarizable empirical force field for hexopyranose monosaccharides based on the classical drude oscillator. J Phys Chem B 119:637–652

    Article  CAS  PubMed  Google Scholar 

  90. Jana M, MacKerell Jr AD (2015) CHARMM Drude polarizable force field for aldopentofuranoses and methyl-aldopentofuranosides. J Phys Chem B 119(25):7846–7859

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Lemkul JA, MacKerell Jr AD (2017) Polarizable force field for DNA based on the classical Drude oscillator: I. refinement using quantum mechanical base stacking and conformational energetics. J Chem Theory Comput 13(5):2053–2071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Lemkul JA, MacKerell Jr AD (2016) Balancing the interactions of Mg(2+) in aqueous solution and with nucleic acid moieties for a polarizable force Field based on the classical Drude oscillator model. J Phys Chem B 120(44):11436–11448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Lopes PEM, Huang J, Shim J, Luo Y, Li H, Roux B et al (2013) Polarizable force field for peptides and proteins based on the classical Drude oscillator. J Chem Theory Comput 9(12):5430–5449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Financial support from the NIH (GM131710) and computational support from the University of Maryland Computer-Aided Drug Design Center are acknowledged.

Author information

Author notes

  1. Abhishek A. Kognole and Asaminew H. Aytenfisu contributed equally to this work.

Authors and Affiliations

  1. University of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA

    Abhishek A. Kognole, Asaminew H. Aytenfisu & Alexander D. MacKerell Jr

Authors
  1. Abhishek A. Kognole
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Asaminew H. Aytenfisu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alexander D. MacKerell Jr
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

ADM, AAK, and AHA conceived the work. AAK and AHA performed the calculations. AAK, AHA, and ADM performed the analysis. AAK, AHA, and ADM wrote and revised the manuscript. AAK and AHA contributed equally.

Corresponding author

Correspondence to Alexander D. MacKerell Jr.

Ethics declarations

Competing interests

ADM Jr. is cofounder and CSO of SilcsBio LLC.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Abhishek A. Kognole and Asaminew H. Aytenfisu are co-first authors

Electronic supplementary material

ESM 1

(PDF 19623 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kognole, A.A., Aytenfisu, A.H. & MacKerell, A.D. Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides. J Mol Model 26, 152 (2020). https://doi.org/10.1007/s00894-020-04399-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-020-04399-0

Keywords

Search

Navigation