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Update usage.rst
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laumalo committed Apr 15, 2021
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Expand Up @@ -104,6 +104,7 @@ arguments. To obtain the full list of flags you can type:
The name of the method to use to compute charges
--charges_from_file PATH
The path to the file with charges
--chain CHAIN Chain of the molecule to parameterize
--include_terminal_rotamers
Not exclude terminal rotamers when building the
rotamer library
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$ python -m peleffy.main path/to/my_ligand.pdb --charges_from_file path/to/my_ligand.mae
Chain
-----
It defines the chain of the molecule to parameterize from the input PDB file.

- Flag: ``--chain``
- Default: ``None``
- Example: the code below will parameterize the hetero molecule in the chain L of the input file

.. code-block:: bash
$ python -m peleffy.main path/to/my_system.pdb --chain L
Include terminal rotamers
-------------------------
It always includes terminal rotamers, even if they belong to a terminal methyl group whose rotation is trivial in PELE.
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