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
Citations
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Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?
Atul Rangadurai,Huiqing Zhou,Dawn K. Merriman,Nathalie Meiser,Bei Liu,Honglue Shi,Eric S. Szymanski,Hashim M. Al-Hashimi +7 more
TL;DR: Insight is provided into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.
Journal ArticleDOI
The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling
TL;DR: The spectral tuning of LH2 antenna complexes arises from H-bonding, acetyl torsion, and inter-chromophore couplings.
Journal ArticleDOI
Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations.
TL;DR: The investigation reveals that tipranavir is the most potent inhibitor against PRCRF while the other three PIs display a similar binding affinity, and can guide the computer-aided rational design of more potent drugs targetting HIV-1PRCRF.
Journal ArticleDOI
Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.
He Huang,Carlos Simmerling +1 more
TL;DR: A novel function to estimate the atomic and molecular SASAs of proteins is developed, which results in comparable accuracy as the LCPO algorithm in reproducing numerical icosahedral-based SASA values.
Journal ArticleDOI
Molecular modelling investigation for drugs and nutraceuticals against protease of SARS-CoV-2.
TL;DR: The idea that existing protease inhibitors and natural compounds could be used to treat the new coronavirus supported by fundamental knowledge as preliminary experimental data provided.
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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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.