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Force Fields for Protein Simulations [chapter]

Jay W. Ponder, David A. Case
2003 Advances in Protein Chemistry  
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

Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Ren
2010 Journal of Computational Chemistry  
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

John D. York, Jay W. Ponder, Z. Chen, F. Scott Mathews, Philip W. Majerus
1994 Biochemistry  
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

Michael J. Dudek, Jay W. Ponder
1995 Journal of Computational Chemistry  
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

Yong Kong, Jay W. Ponder
1997 Journal of Chemical Physics  
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

Daniel J. Kuster, Sergio Urahata, Jay W. Ponder, Garland R. Marshall
2009 Biophysical Journal  
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

Reece K. Hart, Rohit V. Pappu, Jay W. Ponder
2000 Journal of Computational Chemistry  
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
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.
doi:10.1002/(sici)1096-987x(200005)21:7<531::aid-jcc3>;2-c fatcat:s57g7txsyrdjjia5ohalozpizm

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

Pengyu Ren, Jay W. Ponder
2002 Journal of Computational Chemistry  
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

Michael J. Schnieders, Jay W. Ponder
2007 Journal of Chemical Theory and Computation  
., 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

Pengyu Ren, Chuanjie Wu, Jay W. Ponder
2011 Journal of Chemical Theory and Computation  
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: (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

Michael J. Schnieders, Nathan A. Baker, Pengyu Ren, Jay W. Ponder
2007 Journal of Chemical Physics  
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

Andrew C. Simmonett, Frank C. Pickard, Jay W. Ponder, Bernard R. Brooks
2016 Journal of Chemical Physics  
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,
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.
doi:10.1063/1.4964866 pmid:27802661 pmcid:PMC5085973 fatcat:uwkj2pzawvcdlkvdxkbq5o35vu

An efficient newton-like method for molecular mechanics energy minimization of large molecules

Jay W. Ponder, Frederic M. Richards
1987 Journal of Computational Chemistry  
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

Xiange Zheng, Chuanjie Wu, Jay W. Ponder, Garland R. Marshall
2012 Journal of the American Chemical Society  
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

Changsheng Zhang, Chao Lu, Qiantao Wang, Jay W. Ponder, Pengyu Ren
2015 Journal of Chemical Theory and Computation  
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
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.
doi:10.1021/acs.jctc.5b00562 pmid:26574325 pmcid:PMC4768686 fatcat:lqskdoxvpvaxfcrfh6eekoa3am
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