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Force Fields for Protein Simulations
[chapter]
2003
Advances in Protein Chemistry
Preserved Fulltext
For example, a modified Thole water model devised by the Ponder group (Ren and Ponder, 2003) uses atomic polarizabilities of 0.837 Å 3 on oxygen and 0.496 Å 3 on each hydrogen but yields a molecular ...
charge q i at the origin within a molecule whose interior dielectric constant is e in , surrounded by a medium of dielectric constant e out and in which no other charges have yet been placed is then, W ...
doi:10.1016/s0065-3233(03)66002-x
pmid:14631816
fatcat:imkjtojfs5gtrpyqvvu4qzakzi
Multipole electrostatics in hydration free energy calculations
2010
Journal of Computational Chemistry
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According to the work by Ren and Ponder, 33 the quadrupole moments of AMOEBA water molecules were reduced to 73% of the QM DMA values, which led to a reduction of the water-water flap angle to 578 and ...
Cutoff(Å )
Ethylbenze
p-cresol
Isopropanol
imidazole
methylethyl
sulfide
acetic acid
ele
vdW
ele
vdW
ele
vdW
ele
vdW
ele
vdW
ele
vdW
w/LRC
12.0
23.35
2.65
29.37
2.04
28.28 ...
doi:10.1002/jcc.21681
pmid:20925089
pmcid:PMC3073856
fatcat:k6xdzjwigvcjfj6araeuj7b36a
Crystal Structure of Inositol Polyphosphate 1-Phosphatase at 2.3-.ANG. Resolution
1994
Biochemistry
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W. Majerus, and J. D. York, manuscript in preparation. ...
Collection strategies were determined as described by Xuong and colleagues in which w was incremented in 0.1' frames at a rate of 25 s per frame (15 s per frame for low-resolution data). ...
doi:10.1021/bi00249a002
pmid:7947723
fatcat:o2hvc5v3gne35bzozj7cp7x7xi
Accurate modeling of the intramolecular electrostatic energy of proteins
1995
Journal of Computational Chemistry
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This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) CCC 01 92-8651 / 95 1070791 -26 DUDEK AND PONDER accurate representation of electrostatic ...
Change to w or X, might greatly reduce a repulsion that depends on distance as the inverse twelfth power. ...
JOURNAL OF COMPUTATIONAL CHEMISTRY
DUDEK AND PONDER
model [mm3] + [cpk], where the extreme softness
of [mm3] in the region of C, , , ,
combines with the
TABLE XV . ...
doi:10.1002/jcc.540160702
fatcat:bxi47q4pnzfgrfh2hivxi6oqre
Calculation of the reaction field due to off-center point multipoles
1997
Journal of Chemical Physics
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We denote by W i j Ј the RF energy between n 1 th and n 2 th degree multipoles at the same sites. W i j Ј can be considered as a special case of W i j . ...
sϪi y w tϪ j z w uϪk ͩ ץ ץx l M w i jk ͪͬ . ͑29͒ The last two terms of Eq. ͑29͒ come from the local coordinate systems used to define the multipoles at each site. 51 The set L l includes all other ...
doi:10.1063/1.474409
fatcat:uvqzqugngje7ll73bynu5oo2nm
From Data or Dogma? The Myth of the Ideal Helix
2009
Biophysical Journal
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Kuster, Sergio Urahata, Jay W. Ponder, Garland R. Marshall. Washington University in St. Louis, Saint Louis, MO, USA. ...
doi:10.1016/j.bpj.2008.12.918
fatcat:j6w2dxwxznfa3l7vnngtxfde5y
Exploring the similarities between potential smoothing and simulated annealing
2000
Journal of Computational Chemistry
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Simulated annealing and potential function smoothing are two widely used approaches for global energy optimization of molecular systems. Potential smoothing as implemented in the diffusion equation method has been applied to study partitioning of the potential energy surface (PES) for N-Acetyl-Ala-Ala-N-Methylamide (CDAP) and the clustering of conformations on deformed surfaces. A deformable version of the united-atom OPLS force field is described, and used to locate all local minima and
doi:10.1002/(sici)1096-987x(200005)21:7<531::aid-jcc3>3.0.co;2-c
fatcat:s57g7txsyrdjjia5ohalozpizm
more »
... ational transition states on the CDAP surface. It is shown that the smoothing process clusters conformations in a manner consistent with the inherent structure of the undeformed PES. Smoothing deforms the original surface in three ways: structural shifting of individual minima, merging of adjacent minima, and energy crossings between unrelated minima. A master equation approach and explicit molecular dynamics trajectories are used to uncover similar features in the equilibrium probability distribution of CDAP minima as a function of temperature. Qualitative and quantitative correlations between the simulated annealing and potential smoothing approaches to enhanced conformational sampling are established.
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
2002
Journal of Computational Chemistry
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i 2 ͑v i QM Ϫ v i MM ͒ 2 iϭ1 N w i 2 v i QM 2 (12) where the weight w i for each grid point is chosen to be its distance from the closest atom. ...
0.80
2.11
Group 1-2
d
5.51
2.91
3.20
2.55
4.90
3.6
d x
Ϫ3.17
2.90
Ϫ3.11
Ϫ2.45
0.97
5.8
d y
Ϫ1.48
0.17
0.05
0.26
Ϫ4.27
2.5
d z
Ϫ4.25
Ϫ0.23
Ϫ0.76
0.63
2.30
5.8
Ren and Ponder ...
doi:10.1002/jcc.10127
pmid:12395419
fatcat:b42jctpvubcsfpsjlqqzubv3kq
Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum
2007
Journal of Chemical Theory and Computation
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., Vol. 3, No. 6, 2007 Schnieders and Ponder
J. Chem. Theory Comput., Vol. 3, No. 6, 2007 Schnieders and Ponder
J. Chem. Theory Comput., Vol. 3, No. 6, 2007 Schnieders and Ponder
J. ...
Theory Comput., Vol. 3, No. 6, 2007 Schnieders and Ponder ...
doi:10.1021/ct7001336
pmid:26636202
pmcid:PMC4767294
fatcat:fltepj3tdfgd7o5amv3fcfmwcq
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
2011
Journal of Chemical Theory and Computation
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6 373.0 0.984 w
acetamide
13.87
2.42 12.43 13.30 w
198 494.2 0.867 w
N-MeAcet
13.33
0.62 13.44 13.30 dd
30 373.2 0.894 dd
di-MeAcet
8.78
2.16 11.53 11.75 c
349 298.2 0.936 c
methane
0.86 ...
' AUTHOR INFORMATION Corresponding Author *E mail: ponder@dasher.wustl.edu (J.W.P.); pren@mail.utexas. edu (P.R.). ...
doi:10.1021/ct200304d
pmid:22022236
pmcid:PMC3196664
fatcat:gztqd7jkm5f43mvsht5zo26jmu
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum
2007
Journal of Chemical Physics
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conformation is separated into contributions due to nonpolar ⌬W np and electrostatic ⌬W elec effects, ⌬W solvation = ⌬W np + ⌬W elec . ͑1͒ Here we concentrate on the electrostatic contribution, motivated ...
For the permittivity, the switch begins and ends at b = j − w, ͑41͒ e = j + w, where j is the radius of atom j and w indicates how far the smoothing window extends radially inward and outward. ...
An approximate discrete onedimensional realization of this definition ͑approximate because the width is not infinitesimally small͒ is where the function W has been defined in Eq. ͑28͒ via fifth order B-splines ...
doi:10.1063/1.2714528
pmid:17411115
pmcid:PMC2430168
fatcat:fxdg24rji5hwlfr52cmclyqaaq
An empirical extrapolation scheme for efficient treatment of induced dipoles
2016
Journal of Chemical Physics
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Many cutting edge force fields include polarization, to enhance their accuracy and range of applicability. In this work, we develop efficient strategies for the induced dipole polarization method. By fitting various orders of perturbation theory (PT) dipoles to a diverse training set, we arrive at a family of fully analytic methods -whose nth order is referred to OPTn -that span the full spectrum of polarization methods from the fast zeroth-order approach that neglects mutual dipole coupling,
doi:10.1063/1.4964866
pmid:27802661
pmcid:PMC5085973
fatcat:uwkj2pzawvcdlkvdxkbq5o35vu
more »
... proaching the fully variational approach at high order. Our training set contains many difficult cases where the PT series diverges, and we demonstrate that our OPTn methods still deliver excellent results in these cases. Our tests show that the OPTn methods exhibit rapid convergence towards the exact answer with each increasing PT order. The fourth order OPT4 method, whose costs are commensurate with three iterations of the leading conjugate gradient method, is a particularly promising candidate to be used as a drop-in replacement for existing solvers without further parameterization. [http://dx.
An efficient newton-like method for molecular mechanics energy minimization of large molecules
1987
Journal of Computational Chemistry
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Ponder and Richards
COMPUTATIONAL In order to test the efficacy of the Truncated Newton method and compare it with other optimization methods, an explicit potential function and several test cases are ...
As shown in Table IV , the MQN conjugate gradient technique exceeds 7500 cycles and 13000 energy/ Ponder and Richards gradient evaluations before reaching the requested RMS gradient convergence of 10 ...
doi:10.1002/jcc.540080710
fatcat:y6rb7ovklvhobjlyy5hstsblfm
Molecular Dynamics of β-Hairpin Models of Epigenetic Recognition Motifs
2012
Journal of the American Chemical Society
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AMOEBA, a second-generation force field ( Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. ...
Molecular dynamics simulations (100 ns) using the derived parameters with model peptides, such as Ac-R-W-V-W-V-N-G-Orn-K(Me) n -I-L-Q-NH 2 , where n = 0, 1, 2, or 3, were conducted in explicit solvent. ...
doi:10.1021/ja306803v
pmid:22934656
pmcid:PMC3482467
fatcat:sj63udrfgbhl7ng3valc53npha
Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate
2015
Journal of Chemical Theory and Computation
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Phosphate groups are commonly observed in biomolecules such as nucleic acids and lipids. Due to their highly charged and polarizable nature, modeling these compounds with classical force fields is challenging. Using quantum mechanical studies and liquid-phase simulations, the AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl phosphate (TMP) has been developed. On the basis of ab initio calculations, it was found that ion binding and the solution environment significantly impact
doi:10.1021/acs.jctc.5b00562
pmid:26574325
pmcid:PMC4768686
fatcat:lqskdoxvpvaxfcrfh6eekoa3am
more »
... oth the molecular geometry and the energy differences between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ calculations of methyl phosphates at several conformations with their chemical environments taken into account. Many-body polarization is handled via a Thole-style induction model using distributed atomic polarizabilities. van der Waals parameters of phosphate and oxygen atoms are determined by fitting to the quantum mechanical interaction energy curves for water with DMP or TMP. Additional stretch-torsion and angle-torsion coupling terms were introduced in order to capture asymmetry in P−O bond lengths and angles due to the generalized anomeric effect. The resulting force field for DMP and TMP is able to accurately describe both the molecular structure and conformational energy surface, including bond and angle variations with conformation, as well as interaction of both species with water and metal ions. The force field was further validated for TMP in the condensed phase by computing hydration free energy, liquid density, and heat of vaporization. The polarization behavior between liquid TMP and TMP in water is drastically different.
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