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Supported Applications

PDBFixer

  • Description

    an easy to use application that fixes problems in Protein Data Bank files in preparation for simulating. Fixes include: adding missing heavy or hydrogen atoms, building missing loops, convert non-standard residues to their standard equivalents, deleting unwanted heterogens or chains from the model, and building a water box for explicit solvent simulations.

  • Usage

    To list all executables provided by PDBFixer, run: $ sbgrid-list pdbfixer Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install pdbfixer Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, and V. S. Pande. 2013. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory and Computation. ACS Publications. 9(1): 461-469.


    • *Full citation information available through

  • Keywords

    Computational Chemistry

  • Default Versions

    Linux 64:  1.9 (2.3 GB)
    OS X INTEL:  1.9 (291.8 MB)

  • Other Versions

      Linux 64:

      1.8.1 (2.5 GB)

    • OS X INTEL:

      1.8.1 (299.3 MB)

  • Developers

    Peter Eastman

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