Journal ArticleDOI
CHARMM-GUI: a web-based graphical user interface for CHARMM.
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The CHARMM-GUI as mentioned in this paper is a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM.Abstract:
CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery.read more
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Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
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.
Journal ArticleDOI
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.
Robert B. Best,Xiao Zhu,Jihyun Shim,Pedro E. M. Lopes,Jeetain Mittal,Michael Feig,Alexander D. MacKerell +6 more
TL;DR: The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.
Journal ArticleDOI
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
TL;DR: The results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ1 and χ2 dihedral parameters leads to improved treatment of the analyzed nonbond interactions.
Journal ArticleDOI
CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field
Jumin Lee,Xi Cheng,Jason M. Swails,Min Sun Yeom,Peter Eastman,Justin A. Lemkul,Shuai Wei,Joshua Buckner,Jong Cheol Jeong,Yifei Qi,Sunhwan Jo,Vijay S. Pande,David A. Case,Charles L. Brooks,Alexander D. MacKerell,Jeffery B. Klauda,Wonpil Im +16 more
TL;DR: The optimal simulation protocol for each program has been implemented in CHARMM-GUI and is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.
Journal ArticleDOI
CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
Emilia L. Wu,Xi Cheng,Sunhwan Jo,Huan Rui,Kevin C. Song,Eder M. Dávila-Contreras,Yifei Qi,Jumin Lee,Viviana Monje-Galvan,Richard M. Venable,Jeffery B. Klauda,Wonpil Im +11 more
TL;DR: The new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems are described, including addition of new lipid types, including phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol.
References
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Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
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James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
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