Learning to Run Absolute Binding Free Energy  Calculations
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| Zeke A. Piskulich\ :sup:`1`, Patricio Barletta\ :sup:`1`, Ryan Snyder\ :sup:`1`, Harsh Amin\ :sup:`1`, and Darrin M. York\ :sup:`1`
| :sup:`1`\ Laboratory for Biomolecular Simulation Research, Institute
  for Quantitative Biomedicine and Department of Chemistry and Chemical
  Biology, Rutgers University, Piscataway, NJ 08854, USA

Learning objectives
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.. include:: ../../ModularTutorials/ForceField/parameterization_with_LigandParam/tutorial.rst
    :start-after: .. start-learning-objectives
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.. include:: ../../ModularTutorials/ForceField/bespoke_dihedrals_with_FFPOPT/tutorial.rst
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Relevant literature
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Outline
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In this tutorial, we will be using the python package LigandParam, developed by the York Group, to parameterize a ligand for use in molecular dynamics simulations. For this tutorial,
we will be parameterizing the ligand...

Tutorial
--------


.. include:: ../../ModularTutorials/ForceField/parameterizing_ligands_by_hand/tutorial.rst
    :start-after: .. start-tutorial
    :end-before: .. end-tutorial

.. include:: ../../ModularTutorials/Alchemical/ABFE_of_Tyk2/build_binder.rst
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    :end-before: .. end-tutorial

.. include:: ../../ModularTutorials/Alchemical/ABFE_of_Tyk2/equilibrate_endstates.rst
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    :end-before: .. end-tutorial

.. include:: ../../ModularTutorials/Alchemical/ABFE_of_Tyk2/boresch_restraints.rst
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    :end-before: .. end-tutorial

.. include:: ../../ModularTutorials/Alchemical/ABFE_of_Tyk2/anhilate_binder.rst
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    :end-before: .. end-tutorial
    

.. include:: ../../ModularTutorials/Alchemical/ABFE_of_Tyk2/analyzing_abfe.rst
    :start-after: .. start-tutorial
    :end-before: .. end-tutorial

.. include:: ../../ModularTutorials/Alchemical/ABFE_of_Tyk2/tutorial.rst
    :start-after: .. start-tutorial
    :end-before: .. end-tutorial