Calculating Absolute Binding Free Energies of Tyk2 Inhibitors
=============================================================

| Zeke A. Piskulich\ :sup:`1`, Patricio Barletta\ :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
-------------------

.. start-learning-objectives

- Use FFPOPT to Run Dihedral Scans for a Simple Molecule
- Use FFPOPT with a Machine Learning Potential to Fit New Dihedral Parameters

.. end-learning-objectives

Relevant literature
-------------------

- Coming Soon!


Tutorial
--------

.. contents::
   :local:
   :depth: 4

.. start-tutorial


Running ABFE Calculations with AmberFlow
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In this section, we will walk through how to use AmberFlow to set up and run absolute binding free energy calculations (ABFE) for a Tyk2 inhibitor.

The files you will need are located here:

- :download:`Download the tutorial files </_static/files/ModularTutorials/Alchemical/ABFE_of_Tyk2/tutorial_files.tar.gz>`

If you have not already done so, please follow the instructions in the amberflow documentation to install amberflow and set up your environment.

.. warning::

  Currently AmberFlow Documentation is not available online - this should be updated when that changes.


Now, we will walk through the steps to get set up to run ABFE calculations with AmberFlow.

The first step is to unpack the tutorial files; here we will unpack them into a directory called `abfe_tyk2_tutorial`:

.. code-block:: bash

   mkdir abfe_tyk2_tutorial
   cd abfe_tyk2_tutorial
   tar -xvzf ../tutorial_files.tar.gz

In this folder, you will have the following files:








.. end-tutorial