Journal ArticleDOI
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell,D. Bashford,M. Bellott,Roland L. Dunbrack,Jeffrey D. Evanseck,Martin J. Field,Stefan Fischer,Jiali Gao,H. Guo,S. Ha,Diane Joseph-McCarthy,L. Kuchnir,K. Kuczera,F. T. K. Lau,C. Mattos,Stephen W. Michnick,Thien H. Ngo,D. T. Nguyen,B. Prodhom,W. E. Reiher,Benoît Roux,M. Schlenkrich,Jeremy C. Smith,Roland H. Stote,John E. Straub,Masakatsu Watanabe,J. Wiórkiewicz-Kuczera,D. Yin,Martin Karplus +28 more
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TLDR
The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.Abstract:
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...read more
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GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories.
Andreas P. Eichenberger,Jane R. Allison,Jožica Dolenc,Jožica Dolenc,Daan P. Geerke,Bruno A. C. Horta,Katharina Meier,Chris Oostenbrink,Nathan Schmid,Denise Steiner,Dongqi Wang,Wilfred F. van Gunsteren +11 more
TL;DR: These programs are reviewed and the various structural, dynamic, and thermodynamic quantities that can be analyzed using time series, correlation functions, and distributions are described together with technical aspects of their implementation in GROMOS.
Journal ArticleDOI
Biomolecular electrostatics and solvation: a computational perspective.
Pengyu Ren,Jaehun Chun,Dennis G. Thomas,Michael J. Schnieders,Marcelo Marucho,Jiajing Zhang,Nathan A. Baker +6 more
TL;DR: The solvation of biomolecules with a computational biophysics view toward describing the phenomenon is discussed, and the main focus lies on the computational aspect of the models.
Journal ArticleDOI
Metadynamics with adaptive Gaussians
TL;DR: It is illustrated on the case of alanine dipeptide the advantage of using adaptive Gaussians in conjunction with the new free-energy estimator both in terms of accuracy and speed of convergence.
Journal ArticleDOI
Quantum Dynamics of Hydride Transfer in Enzyme Catalysis
TL;DR: In this article, an elevated Swain−Schaad exponent for the secondary kinetic isotope effect in the hydride-transfer step catalyzed by liver alcohol dehydrogenase was found.
Journal ArticleDOI
Identifying unfolding intermediates of FN-III10 by steered molecular dynamics
TL;DR: Three forced unfolding pathways of FN-III(10), one of which is preferentially selected under physiological conditions are revealed, and implications for fibronectin fibrillogenesis are discussed.
References
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Journal ArticleDOI
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Journal ArticleDOI
Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Journal ArticleDOI
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.