We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

/pdf/the-amber-biomolecular-simulation-programs-e2nyq1ef44.pdf

The Amber biomolecular simulation programs

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/prot.22711

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

A potential model intended to be a general purpose model for the condensed phases of water is presented. TIP4P/2005 is a rigid four site model which consists of three fixed point charges and one Lennard-Jones center. The parametrization has been based on a fit of the temperature of maximum density (indirectly estimated from the melting point of hexagonal ice), the stability of several ice polymorphs and other commonly used target quantities. The calculated properties include a variety of thermodynamic properties of the liquid and solid phases, the phase diagram involving condensed phases, properties at melting and vaporization, dielectric constant, pair distribution function, and self-diffusion coefficient. These properties cover a temperature range from 123to573K and pressures up to 40000bar. The model gives an impressive performance for this variety of properties and thermodynamic conditions. For example, it gives excellent predictions for the densities at 1bar with a maximum density at 278K and an aver...

http://cacharro.quim.ucm.es/publicaciones/JCP_123_234505_2005.pdf

A general purpose model for the condensed phases of water: TIP4P/2005

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within t...

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

When Szent-Gyorgyi called water the “matrix of life”,1 he was echoing an old sentiment. Paracelsus in the 16th century said that “water was the matrix of the world and of all its creatures.”2 But Paracelsus’s notion of a matrixsan active substance imbued with fecund, life-giving propertiess was quite different from the picture that, until very recently, molecular biologists have tended to hold of water’s role in the chemistry of life. Although acknowledging that liquid water has some unusual and important physical and chemical propertiessits potency as a solvent, its ability to form hydrogen bonds, its amphoteric naturesbiologists have regarded it essentially as the backdrop on which life’s molecular components are arrayed. It used to be common practice, for example, to perform computer simulations of biomolecules in a vacuum. Partly this was because the computational intensity of simulating a polypeptide chain was challenging even without accounting for solvent molecules too, but it also reflected the prevailing notion that water does little more than temper or moderate the basic physicochemical interactions responsible for molecular biology. What Gerstein and Levitt said 9 years ago remains true today: “When scientists publish models of biological molecules in journals, they usually draw their models in bright colors and place them against a plain, black background”.3 Curiously, this neglect of water as an active component of the cell went hand in hand with the assumption that life could not exist without it. That was basically an empirical conclusion derived from our experience of life on Earth: environments without liquid water cannot sustain life, and special strategies are needed to cope with situations in which, because of extremes of either heat or cold, the liquid is scarce.4-6 The recent confirmation that there is at least one world rich in organic molecules on which rivers and perhaps shallow seas or bogs are filled with nonaqueous fluidsthe liquid hydrocarbons of Titan7smight now bring some focus, even urgency, to the question of whether water is indeed a * E-mail: p.ball@nature.com. Philip Ball is a science writer and a consultant editor for Nature, where he worked as an editor for physical sciences for more than 10 years. He holds a Ph.D. in physics from the University of Bristol, where he worked on the statistical mechanics of phase transitions in the liquid state. His book H2O: A Biography of Water (Weidenfeld & Nicolson, 1999) was a survey of the current state of knowledge about the behavior of water in situations ranging from planetary geomorphology to cell biology. He frequently writes about aspects of water science for both the popular and the technical media.

https://www.philipball.co.uk/images/stories/docs/pdf/ChemRev_final.pdf

Water as an Active Constituent in Cell Biology

A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at approximately 1 degrees C, and reproduces experimental bulk-densities and the enthalpy of vaporization, DeltaH(vap), from -37.5 to 127 degrees C at 1 atm with an absolute average error of less than 1%. Structural properties are in very good agreement with x-ray scattering intensities at temperatures between 0 and 77 degrees C and dynamical properties such as self-diffusion coefficient are in excellent agreement with experiment. The parameterization approach used can be easily generalized to rehabilitate any water force field using available experimental data over a range of thermodynamic points.

/pdf/development-of-an-improved-four-site-water-model-for-10rw432kke.pdf

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

/pdf/water-structure-from-scattering-experiments-and-simulation-28vet218uw.pdf

Water structure from scattering experiments and simulation.

We present an analysis of the Advanced Light Source (ALS) x-ray scattering experiment on pure liquid water at ambient temperature and pressure described in the preceding article. The present study discusses the extraction of radial distribution functions from the x-ray scattering of molecular fluids. It is proposed that the atomic scattering factors used to model water be modified to include the changes in the intramolecular electron distribution caused by chemical bonding effects. Based on this analysis we present a gOO(r) for water consistent with our recent experimental data gathered at the ALS, which differs in some aspects from the gOO(r) reported by other x-ray and neutron scattering experiments. Our gOO(r) exhibits a taller and sharper first peak, and systematic shifts in all peak positions to smaller r. Based on experimental uncertainties, we discuss what features of gOO(r) should be reproduced by classical simulations of nonpolarizable and polarizable water models, as well as ab initio simulations of water, at ambient conditions. We directly compare many water models and simulations to the present data, and discuss possible improvements in both classical and ab initio simulation approaches in the future.

What can x-ray scattering tell us about the radial distribution functions of water?

We report a new, high-quality x-ray scattering experiment on pure ambient water using a synchrotron beam line at the Advanced Light Source at Lawrence Berkeley National Laboratory. Several factors contribute to the improved quality of our intensity curves including use of a highly monochromatic source, a well-characterized polarization correction, a Compton scattering correction that includes electron correlation, and more accurate intensities using a modern charge coupled device (CCD) detector. We provide a comprehensive description of the data processing that we have used for correcting systematic errors, and we provide an estimate of our remaining random errors. The resulting error estimates of our data are smaller then the discrepancies between data sets collected in past x-ray experiments. We find that the older x-ray curves support a family of gOO(r)’s that exhibit a smaller first peak (∼2.2), while the current data is better fit with a family of gOO(r)’s with a first peak height of 2.8, and systema...

A high-quality x-ray scattering experiment on liquid water at ambient conditions

Structural polyamorphism has been promoted as a means for understanding the anomalous thermodynamics and dynamics of water in the experimentally inaccessible supercooled region. In the metastable liquid region, theory has hypothesized the existence of a liquid-liquid critical point from which a dividing line separates two water species of high and low density. A recent small-angle X-ray scattering study has claimed that the two structural species postulated in the supercooled state are seen to exist in bulk water at ambient conditions. We analyze new small-angle X-ray scattering data on ambient liquid water taken at third generation synchrotron sources, and large 32,000 water molecule simulations using the TIP4P-Ew model of water, to show that the small-angle region measures standard number density fluctuations consistent with water’s isothermal compressibility temperature trends. Our study shows that there is no support or need for heterogeneities in water structure at room temperature to explain the small-angle scattering data, as it is consistent with a unimodal density of the tetrahedral liquid at ambient conditions.

https://www.pnas.org/content/pnas/107/32/14003.full.pdf

Greg L. Hura

Papers

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

Water structure from scattering experiments and simulation.

What can x-ray scattering tell us about the radial distribution functions of water?

A high-quality x-ray scattering experiment on liquid water at ambient conditions

Small-angle scattering and the structure of ambient liquid water