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CHARMM-GUI: A web-based graphical user interface for CHARMM

  1. Sunhwan Jo1,
  2. Taehoon Kim2,
  3. Vidyashankara G. Iyer1,
  4. Wonpil Im2,*

Article first published online: 19 MAR 2008

DOI: 10.1002/jcc.20945

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 29, Issue 11, pages 1859–1865, August 2008

Additional Information

How to Cite

Jo, S., Kim, T., Iyer, V. G. and Im, W. (2008), CHARMM-GUI: A web-based graphical user interface for CHARMM. J. Comput. Chem., 29: 1859–1865. doi: 10.1002/jcc.20945

Author Information

  1. 1

    Department of Chemistry, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047

  2. 2

    Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047

*Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047

Publication History

  1. Issue published online: 10 JUN 2008
  2. Article first published online: 19 MAR 2008
  3. Manuscript Accepted: 14 JAN 2008
  4. Manuscript Revised: 17 DEC 2007
  5. Manuscript Received: 2 NOV 2007

Funded by

  • University of Kansas

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Keywords:

  • molecular dynamics;
  • Poisson-Boltzmann;
  • electrostatic potential;
  • membrane;
  • visualization;
  • explicit solvent;
  • implicit solvent;
  • MarvinSpace

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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008

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