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PDBFixer Documentation

repository·master·Indexed 20 days ago

https://github.com/openmm/pdbfixer

A utility for preparing Protein Data Bank (PDB) files for molecular simulations. PDBFixer automatically resolves structural deficiencies by adding missing heavy and hydrogen atoms, building missing loops, converting non-standard residues, resolving alternate atom positions, removing unwanted chains or heterogens, and building water boxes for explicit solvent simulations.

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What's inside PDBFixer

  1. Overview of PDBFixer capabilities

    master

    PDBFixer is a tool designed to prepare Protein Data Bank (PDB) files for molecular simulations by automatically resolving common structural issues.

    Key features include:

    • Adding missing heavy atoms and hydrogen atoms.
    • Building missing loops.
    • Converting non-standard residues to standard equivalents.
    • Resolving alternate atom positions by selecting a single position.
    • Removing unwanted chains or heterogens.
    • Building water boxes for explicit solvent simulations.