Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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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Journal ArticleDOI
DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site
TL;DR: This study suggests that the association of H-DNA is a concerted process, where Hoechst 33258 cooperates with DNA single strands in forming H- DNA.
Journal ArticleDOI
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.
Nigel W. Moriarty,Pawel A. Janowski,Jason M. Swails,Hai Nguyen,Jane S. Richardson,David A. Case,Paul D. Adams,Paul D. Adams +7 more
TL;DR: The full Amber force field has been integrated into Phenix as an alternative refinement target, with a slight loss in speed, that achieves improved stereochemistry, fewer steric clashes and better hydrogen bonds.
Journal ArticleDOI
Computational Studies of Intrinsically Disordered Proteins
TL;DR: In short peptide simulations, a tested IDP-specific force field ff14IDPSFF outperforms its generic counterpart ff14SB as agreement of simulated NMR observables with experiment improves, though its advantages are not clear-cut in apo Rev simulations.
Journal ArticleDOI
Making it Rain: Cloud-Based Molecular Simulations for Everyone.
TL;DR: In this paper, the authors present a front-end for running molecular dynamics simulations using the OpenMM toolkit on the Google Colab framework and demonstrate how low-income research groups can perform MD simulations in the microsecond time scale.
Journal ArticleDOI
Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better?
TL;DR: An intermediate approach relying on classical MD followed by a constrained QM/MM geometry optimization to be a fairly accurate and very cost-effective approach, although this procedure naturally leads to underestimation of, for example, spectral bandwidths.
References
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VMD: Visual molecular dynamics
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Journal ArticleDOI
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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.
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Journal ArticleDOI
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