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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.

  • 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, Utilities

  • Default Versions

    Linux 64:  20151011
    OS X INTEL:  20151011

  • Other Available Versions

      Linux 64:

      1.3
    • OS X INTEL:

      1.3
  • Developers

    Peter Eastman, Vijay Pande.

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