Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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TLDR
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...read more
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Phase separation property of a hydrophobic deep eutectic solvent-water binary mixture: A molecular dynamics simulation study.
TL;DR: In this paper, the phase separation properties of a 1:1 mixture of oleic acid and lidocaine solvents in aqueous solution were studied at three different temperatures (253, 293, and 313 K).
Journal ArticleDOI
Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale.
TL;DR: The model of static canonical structures is extended to a dynamic conformational ensemble as a new paradigm in the field of antibody structure design to reconstruct the kinetics and probabilities of the transitions between canonical structures.
Journal ArticleDOI
Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics.
Jian Wang,Yinglong Miao +1 more
TL;DR: PPI-GaMD provides a highly efficient and easy-to-use approach for binding free energy and kinetics calculations of PPIs and provides mechanistic insights into barstar binding to barnase, which involves long-range electrostatic interactions and multiple binding pathways.
Journal ArticleDOI
Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with S-adenosylmethionine
TL;DR: This work presents an approach that refines the highly accurate PANIC NMR methodology combined with clustering approaches to generate conformers, but without restraining the simulations or considering the relative population distributions generated by MD.
Journal ArticleDOI
Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases
Dirk Maurer,Thilak Reddy Enugala,Emil Hamnevik,Paul Bauer,Paul Bauer,Malin Lüking,Dušan Petrović,Heidi Hillier,Shina Caroline Lynn Kamerlin,Doreen Dobritzsch,Mikael Widersten +10 more
TL;DR: ADH-A from Rhodococcus ruber DSM 44541 catalyzes the oxidation of (S)-1-phenylethanol 3000-fold more efficiently as compared with the 2-hydroxylated derivative (R)-phenylethane-1,2-diol, suggesting a shift from a less active enzyme.
References
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VMD: Visual molecular dynamics
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.
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
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.
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The Amber biomolecular simulation programs
David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
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.
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Journal ArticleDOI
General definition of ring puckering coordinates
Dieter Cremer,John A. Pople +1 more
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.