=======================
Input files preparation
=======================

PELE Platform essentially needs a minimum of two files in order to run:

    - ``system.pdb``: a PDB file that contains the structure to simulate with PELE.
      It typically contains a protein and a small molecule.
    - ``input.yaml``: a yaml file containing a collection of parameters to
      set up the simulation.

.. image:: ../img/platform_flow.png
  :align: center

Additionally, although the Platform can create them automatically, we might
want to supply custom templates for our ligand or other non standard residues.

    - ``templates``: optionally, we can supply parameter templates or rotamer
      libraries for specific non standard residues.

Below we list several instructions to correctly prepare input PDB files for PELE:

.. toctree::
   :maxdepth: 2

   system_preparation.rst


On the other hand, the list of all parameters that can be specified in the
``input.yaml`` file can be found below:

.. toctree::
   :maxdepth: 2

   yaml.rst

Finally, the instructions to manage custom templates are:

.. toctree::
   :maxdepth: 2

   templates.rst