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01_introduction/02_molecular_setup.ipynb

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"If pre-processing of the PDB file is required, then we recommend using one of the following third-party tools:\n",
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"* [pdb4amber](https://github.com/Amber-MD/pdb4amber)\n",
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"* [pdb4amber](https://ambermd.org/tutorials/basic/tutorial9/index.php)\n",
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"* [PDBFixer](https://htmlpreview.github.io/?https://github.com/openmm/pdbfixer/blob/master/Manual.html)\n",
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"When present, we do provide rudimentary support for `pdb4amber` via the `BioSimSpace.IO.reaadPDB` function, where passing the `pdb4amber=True` argument will pre-process the file with `pdb4amber` prior to creating a molecular system. However, we choose only to support the _default_ options, since many are experimental and can have undesirable knock-on effects, e.g. using the `--add-missing-atoms` option strips all chain identifiers from the molecule.\n",

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