Hands-On Session 13: Using AmberStudio to Perform Alchemical Free Energy Simulations
=====================================================================================
| German P. Barletta\ :sup:`1`, Zeke A. Piskulich\ :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
-------------------

.. include:: /ModularTutorials/Alchemical/AmberStudio/intro.rst
    :start-after: .. start-learning-objectives
    :end-before: .. end-learning-objectives

.. include:: /ModularTutorials/Alchemical/AmberStudio/system-builds.rst
    :start-after: .. start-learning-objectives
    :end-before: .. end-learning-objectives

.. include:: /ModularTutorials/Alchemical/AmberStudio/free-md.rst
    :start-after: .. start-learning-objectives
    :end-before: .. end-learning-objectives

.. include:: /ModularTutorials/Alchemical/AmberStudio/abfe_example.rst
    :start-after: .. start-learning-objectives
    :end-before: .. end-learning-objectives

.. include:: /ModularTutorials/Alchemical/AmberStudio/rbfe-example.rst
    :start-after: .. start-learning-objectives
    :end-before: .. end-learning-objectives

Activities
----------

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

.. mermaid::

    flowchart LR

    %% ===== inputs =====
    A1["Input structures<br/>binder_ejm31.pdb<br/>target_ejm31.pdb"]

    %% ===== concepts =====
    C1{{"<b>[§13.2.1]</b><br/>Concepts: Artifacts<br/>WorkNodes, Flows, Pipelines"}}

    %% ===== ligand parameters =====
    P2{{"<b>[§13.2.2]</b><br/>Generate ligand parameters<br/>ParametrizeBinderBCC"}}
    O2["<b>[from §13.2.2]</b><br/>Ligand parameters<br/>binder.mol2 / .lib / .frcmod"]

    %% ===== build systems =====
    P3{{"<b>[§13.2.3]</b><br/>Build solvated systems<br/>FlowBuild"}}
    O3["<b>[from §13.2.3]</b><br/>Built systems<br/>complex/binder .parm7 / .rst7"]

    %% ===== free-MD =====
    P4a{{"<b>[§13.2.4.1]</b><br/>Equilibrate system<br/>FlowRoeRelax"}}
    P4b{{"<b>[§13.2.4.2]</b><br/>Append free MD<br/>MDRun"}}
    O4["<b>[from §13.2.4]</b><br/>Equilibrated system<br/>MD trajectory .nc"]

    %% ===== ABFE =====
    P5{{"<b>[§13.2.5]</b><br/>Absolute binding free energy<br/>FlowABFEProduction"}}
    O5["<b>[from §13.2.5]</b><br/>Binding free energy<br/>delta-G report"]

    %% ===== RBFE =====
    P6a{{"<b>[§13.2.6.1]</b><br/>Build RBFE edges<br/>AmberStudio"}}
    P6b{{"<b>[§13.2.6.2]</b><br/>Run RBFE edges<br/>AmberStudio"}}
    O6["<b>[from §13.2.6]</b><br/>Relative binding free energy<br/>delta-delta-G"]

    C1 --> A1
    A1 --> P2
    P2 --> O2
    O2 --> P3
    P3 --> O3
    O3 --> P4a
    P4a --> P4b
    P4b --> O4
    O4 --> P5
    P5 --> O5
    O4 --> P6a
    P6a --> P6b
    P6b --> O6

    classDef file fill:#fff7e6,stroke:#d98c00,stroke-width:1.5px,color:#111;
    classDef program fill:#e8f1ff,stroke:#1f77b4,stroke-width:1.8px,color:#111;
    classDef result fill:#eaf7ea,stroke:#2ca02c,stroke-width:1.5px,color:#111;
    class A1 file;
    class C1,P2,P3,P4a,P4b,P5,P6a,P6b program;
    class O2,O3,O4,O5,O6 result;

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

.. include:: /ModularTutorials/Alchemical/AmberStudio/system-builds.rst
    :start-after: .. start-tutorial
    :end-before: .. end-tutorial

.. include:: /ModularTutorials/Alchemical/AmberStudio/free-md.rst
    :start-after: .. start-tutorial
    :end-before: .. end-tutorial


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


.. include:: /ModularTutorials/Alchemical/AmberStudio/rbfe-example.rst
    :start-after: .. start-tutorial
    :end-before: .. end-tutorial



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

.. footbibliography::