317
Views
6
CrossRef citations to date
0
Altmetric
Articles

Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling

, &
Pages 912-921 | Received 26 Mar 2013, Accepted 05 Jul 2013, Published online: 03 Sep 2013

References

  • DillKA. Dominant forces in protein folding. Biochemistry. 1990;29:7133.
  • MaoAH, LyleN, PappuRV. Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J. 2013;449:307–318.
  • KitaoA, HirataF, GoN. The effects of solvent on the conformation and the collective motions of protein – normal mode analysis and molecular-dynamics simulations of melittin in water and in vacuum. Chem Phys. 1991;158:447.
  • CramerCJ, TruhlarDG. Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem Rev. 1999;99:2161–2200.
  • LazaridisT, KarplusM. Effective energy functions for protein structure prediction. Curr Opin Struct Biol. 2000;10:139–145.
  • BashfordD, CaseDA. Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem. 2000;51:129–152.
  • FennellCJ, DillKA. Physical modeling of aqueous solvation. J Stat Phys. 2011;145:209.
  • LopesPEM, RouxB, MacKerellADJr. Accurate calculation of hydration free energies using pair-specific Lennard-Jones parameters in the CHARMM Drude polarizable force field. Theor Chem Acc. 2009;124:11–28.
  • JorgensenWL, ChandrasekharJ, MaduraJD, ImpeyRW, KleinML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926.
  • WuY, TepperHL, VothGA. Flexible simple point-charge water model with improved liquid-state properties. J Chem Phys. 2006;124:024503.
  • BerendsenHJC, PostmaJP, van GunsterenWF, HermansJ. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht: Reidel; 1981. p. 331.
  • MacKerellADJr., BashfordD, BellottM, DunbrackRL, EvanseckJD, FieldMJ, FischerS, GaoJ, GuoH, HaS, Joseph-McCarthyD, KuchnirL, KuczeraK, LauFTK, MattosC, MichnickS, NgoT, NguyenDT, ProdhomB, ReiherWE, RouxB, SchlenkrichM, SmithJC, StoteR, StraubJ, WatanabeM, Wiorkiewicz-KuczeraJ, YinD, KarplusM. All atom empirical potential for molecular modelling and dynamics studies of proteins. J Phys Chem B. 1998;102:3586.
  • BrooksBR, BruccoleriRE, OlfasonBD, StatesDJ, SwaminathanS, KarplusM. CHARMM – a program for macromolecular energy, minimization and dyanmics calculations. J Comput Chem. 1983;4:187.
  • PearlmanDA, CaseDA, CaldwellJW, RossWS, CheathamTEIII, DeBoltS, FergusonD, SeibelG, KollmanP. AMBER, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun. 1995;91:1.
  • CornellWD, CieplakP, BaylyCI, GouldIR, MerzJKM, FergusonDM, SpellmeyerDC, FoxT, CaldwellJW, KollmanPA. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc. 1995;117:5179.
  • JorgensenWL, Tirado-RivesJ. The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc. 1988;110:1657.
  • JorgensenWL, MaxwellDS, Tirado-RivesJ. Development and testing of the OPLS All-atom forcefield on conformational energectic and properties of organic liquids. J Am Chem Soc. 1996;118:11225.
  • van GunsterenWF, BerendsenHJC. Gromos-87 Manual Biomos BV Nijenborgh 4, 9747 AG Groningen. The Netherlands; 1987.
  • van GunsterenWF, BilleterSR, EisingAA, HünenbergerPH, KrügerP, MarkAE, ScottWRP, TironiIG. Biomolecular Simulation: GROMOS96 Manual and User Guide, Zürich, Switzerland: Vdf Hochschulverlag AG an der ETH Zürich; 1996.
  • NeriaE, FisherS, KarplusM. Simulation of activation free energies in molecular dynamics. J Chem Phys. 1996;105:1902.
  • GlassDC, KrishnanM, NuttDR, SmithJC. Temperature dependence of protein dynamics simulated with three different water models. J Chem Theor Comput. 2010;6:1390.
  • ZhangC, RaugeiS, EisenbergB, CarloniP. Molecular dynamics in physiological solutions: force fields, alkali metal ions, and ionic strength. J Chem Theor Comput. 2010;6:2167.
  • AgarwalM, KushwahaHR, ChakravartyC. Local order, energy, and mobility of water molecules in the hydration shell of small peptides. J Phys Chem. 2010;114:651.
  • TakemuraK, KitaoA. Effects of water model and simulation box size on protein diffusional motions. J Phys Chem Lett B. 2007;111:11870.
  • PaschekD, DayR, GarciaAE. Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models. Phys Chem Chem Phys. 2011;13:19840.
  • WuC, ChenM, GuoC, ZhaoX, YuanC. Peptide–TiO2 interaction in aqueous solution: conformational dynamics of RGD using different water models. J Phys Chem B. 2010;114:4692.
  • RaiteriP, GaleJD. Water is the key to nonclassical nucleation of amorphous calcium carbonate. J Am Chem Soc. 2010;132:17623.
  • FreemanCL, HardingJH, QuigleyD, RodgerPM. Structural control of crystal nuclei by an eggshell protein. Angew Chem Int Ed. 2010;49:5135–5137.
  • FreemanCL, HardingJH, QuigleyD, RodgerPM. Simulations of ovocleidin-17 binding to calcite surfaces and its implications for eggshell formation. J Phys Chem C. 2011;115:8175–8183.
  • RaiteriP, DemichelisR, GaleJD, KellermeierM, GebauerD, QuigleyD, WrightLB, WalshTR. Exploring the influence of organic species on pre and post-nucleation calcium carbonate. Faraday Discuss. 2012;159:61.
  • SugitaY, OkamotoY. Replica-exchange molecular dynamics method for protien folding. Chem Phys Lett. 1999;314:141.
  • LowerBH, LinsRD, OestreicherZ, StraatsmaTP, HochellaMF, ShiL, LowerSK. In vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype. Environ Sci Technol. 2008;42:3821–3827.
  • HessB, KutznerC, van der SpoelD, LindahlE. Gromacs 4: algorithms for highly efficient, load balanced, and scable molecular simulation. J Chem Theor Comput. 2008;4:435.
  • PonderJW, RenP, PappuRV, HartRK, HodgsonME, CistolaDP, KundrotCE, RichardsFM. TINKER – software tools for molecular design. Washington University School of Medicine, Version 6.2 edn.2013.
  • BerendsenHJC, PostmaJPM, van GunsterenWF, DiNolaA, HaakJR. Molecular-dynamics with coupling to an external bath. J Chem Phys. 1984;81:3684.
  • NoséS. A molecular-dynamics method for simulations in the canonical ensemble. Mol Phys. 1984;52:255.
  • HooverWG. Canonical dynamics – equilibrium phase-space distributions. Phys Rev A. 1985;31:1695.
  • PatrikssonA, van der SpoelD. A temperature predictor for parallel tempering simulations. Phys Chem Chem Phys. 2008;10:2073.
  • DauraX, GademannK, JaunB, SeebachD, van GunsterenWF, MarkAE. Peptide folding: when simulation meets experiment. Angew Chem Int Ed. 1999;38:236.
  • ParrinelloM, RahmanA. Polymorphic transitions in single-crystals – a new molecular-dynamics method. J Appl Phys. 1981;52:7182.
  • NoséS, KleinML. Constant pressure molecular-dynamics for molecular-systems. Mol Phys. 1983;52:7182.
  • AllenMP, TildesleyDJ. Computer simulation of liquids. Oxford: Oxford University Press; 1987.
  • DardenT, YorkD, PedersenL. Particle mesh Ewald – an n·log(n) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089.
  • PetersenHG. Accuracy and efficiency of the particle mesh Ewald method. J Chem Phys. 1995;103:3668.
  • EssmannU, PereraL, BekowitzML, DardenT, LeeH, PedersenLG. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577.
  • FellerSE, PastorRW, RojnuckarinA, BoguszS, BrooksBR. Effect of electrostatic force truncation on interfacial and transport properties of water. J Phys Chem. 1996;100:17011.
  • SchulzJCF, SchmidtL, BestRB, DzubiellaJ, NetzRR. Peptide chain dynamics in light and heavy water: zooming in on internal friction. J Am Chem Soc. 2012;134:6273.
  • LeungK, RempeSB. Ab initio molecular dynamics study of formate ion hydration. J Am Chem Soc. 2004;126:344.
  • HugossonHW, LaioA, MaurerP, RothlisbergerU. A comparative theoretical study of dipeptide solvation in water. J Comput Chem. 2006;27:672.
  • LiangT, WalshTR. Molecular dynamics simulations of peptide carboxylate hydration. Phys Chem Chem Phys. 2006;8:4410.
  • LiangT, WalshTR. Simulation of the hydration structure of glycyl-alanine. Mol Simul. 2007;33:337.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.