PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
25 Jun 2013-Journal of Chemical Theory and Computation (American Chemical Society)-Vol. 9, Iss: 7, pp 3084-3095
TL;DR: PTRAJ and its successor CPPTRAJ are described, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions and the data therein derived.
Abstract: We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambe...
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TL;DR: Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution.
Abstract: Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple sm...
6,367 citations
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TL;DR: This work presents PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++), which introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs.
2,256 citations
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TL;DR: MDTraj is a modern, lightweight, and fast software package for analyzing MD simulations that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
1,480 citations
Cites methods from "PTRAJ and CPPTRAJ: Software for Pro..."
...Several other software packages for the analysis of MD trajectories exist, including the GROMACS tools (6), CPPTRAJ (7), VMD (8), MMTK (9), MDAnalysis (10), Bio3D (11), ST-Analyzer (12), LOOS (13), and Pteros (14)....
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TL;DR: The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package, and is compatible with theAMBER protein, nucleic acid, carbohydrate, and small molecule force fields.
Abstract: The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields.
973 citations
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TL;DR: The types of information molecular dynamics simulations can provide and the ways in which they typically motivate further experimental work are described.
964 citations
References
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TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
46,130 citations
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TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Abstract: For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.
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TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which 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.
Abstract: 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.
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TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.
7,035 citations
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TL;DR: In this article, a unique mean plane is defined for a general monocyclic puckered ring, which is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer.
Abstract: A unique mean plane is defined for a general monocyclic puckered ring. The geometry of the puckering relative to this plane is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer. Unlike earlier treatments based on torsion angles, no mathematical approximations are involved. A short treatment of the four-, five-, and six-membered ring demonstrates the usefulness of this concept. Finally, an example is given of the analysis of crystallographic structural data in terms of these coordinates. Although the nonplanar character of closed rings in many cyclic compounds has been widely recognized for many years, there remain some difficulties in its quantitative specification. An important first step was taken by Kilpatrick, Pitzer, and Spitzer in their 1947 discussion of the molecular structure of cyclopentane.' Starting with the normal modes of out-of-plane motions of a planar regular pentagon,* they pointed out that displacement of the j t h carbon atom perpendicular to the plane could be written 2 112 zj = (/'SI 4 COS (2+ + 4 n ( j 11/51 (11 where q is a puckering amplitude and $ is a phase angle describing various kinds of puckering. By considering changes in an empirical potential energy for displacements perpendicular to the original planar form, they gave reasons to believe that the lowest energy was obtained for a nonzero value of q (finite puckering) but that this minimum was largely independent of $. Motion involving a change in fi at constant q was described as pseudorotation. Subsequent refinement of this work has involved models in which constraints to require constant bond lengths are imposed3q4 and extensions to larger rings5-' and some heterocyclic systems are considered.* Although the correctness of the model of Kilpatrick, et a f . , I and the utility of the (q. $) coordinate system is generally accepted, application to a general five-membered ring with unequal bond lengths and angles is not straightforward. Given the Cartesian coordinates for the five atoms (as from a crystal structure), determination of puckering displacements z, requires specification of the plane z = 0. A least-squares choice (minimization of Zz i2) is one possibility, but the five displacements relative to this plane cannot generally be expressed in terms of two parameters q and $ according to eq 1. An attempt to define a generalized set of puckering cordinates which avoids these difficulties was made by Geise, Altona, Romers, and S~ndara l ingam.~l ' Their quantitative description of puckering in five-membered rings involves the five torsion angles 0, rather than displacements perpendicular to some plane. These torsion angles are directly derivable from the atomic coordinates and are all zero in the planar form. They proposed a relationship of the form\
6,526 citations