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Namdinator

  • Description

    a commandline tool, written in BASH, that sets up and runs a MDFF (molecular Dynamics Flexible Fit) simulation in a semi automatic manner, using only the input PDB file and input density file.

  • Usage

    To list all executables provided by Namdinator, run: $ sbgrid-list namdinator Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install namdinator Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    R. T. Kidmose, J. Juhl, P. Nissen, T. Boesen, J. L. Karlsen, and B. P. Pedersen. 2019. Namdinator - automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps. IUCrJ. 6(4): 526-531.


    • *Full citation information available through

  • Keywords

    Computational Chemistry

  • Default Versions

    Linux 64:  20191016-5814c947 (63.9 MB)

  • Developers

    Jesper Lykkegaard Karlsen, Rune Kidmose

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