**Running OpenMMDL Setup**
=============================

This page displays the preparation paths and forcefields available in **OpenMMDL** and showcases the application of **OpenMMDL Setup**.

.. figure:: /_static/images/OpenMMDL_Setup.png
    :figwidth: 600px
    :height: 100px
    :align: center
|  
To start the **OpenMMDL Setup** we need to activate the `openmmdl` environment. To do this we have to enter the following command lines:

.. code-block:: text

    conda activate openmmdl

Now that we have activated the `openmmdl` environment we can start **OpenMMDL Setup**. To do this you need to type the following:

.. code-block:: text

    openmmdl setup

This will open the **OpenMMDL Setup**, which you can use for the creation of the input files for **OpenMMDL Simulation**.

There are two possible options to create the input files for **OpenMMDL Simulation**:

1. The PDBFixer path, where a `pdb` file of the protein is used as an input for the preparation and simulation.
The tutorial for the PDBFixer path can be found :doc:`here </tutorial_pdb_path>`.

Here is the table of the currently available forcefields and water models for the PDBFixer path: 

.. list-table:: PDBFixer path AMBER forcefields
   :header-rows: 1
   :widths: 26 34 34

   * - Water model
     - AMBER14 / AMBER19
     - AMBER99SB / AMBER99SB-ILDN / AMBER03 / AMBER10
   * - TIP3P
     - ✓
     - ✓
   * - TIP3P-FB
     - ✓
     - ✓
   * - SPC/E
     - ✓
     - ✓
   * - TIP4P-Ew
     - ✓
     - ✓
   * - TIP4P-FB
     - ✓
     - —
   * - TIP5P
     - —
     - ✓
   * - OPC3
     - ✓
     - ✓
   * - OPC
     - ✓
     - ✓


.. list-table:: PDBFixer path CHARMM forcefields
   :header-rows: 1
   :widths: 34 34 34

   * - Water model
     - CHARMM36
     - CHARMM36 2024
   * - SPC/E
     - ✓
     - ✓
   * - TIP4P-Ew
     - ✓
     - ✓
   * - TIP5P
     - ✓
     - ✓
   * - CHARMM default
     - ✓
     - ✓
   * - TIP3P-PME-B
     - ✓
     - ✓
   * - TIP3P-PME-F
     - ✓
     - ✓
   * - TIP4P-2005
     - ✓
     - ✓
   * - TIP5P-Ew
     - ✓
     - ✓

2. The Amber path, where `prmtop` and `inpcrd` files are used the preparation and simulation. This path allows us to either use already prepared `prmtop` and `inpcrd` as an input or create the `prmtop` and `inpcrd` from PDB files of the receptor and ligand.
The tutorial for the Amber path can be found :doc:`here </tutorial_amber_path>`.

.. figure:: /_static/images/amber_ff.png
   :figwidth: 725px
   :align: center

In the table, the first row is the default setting, and the term `other` allows users to type their desired forcefields from those accessible in AmberTools 22.0 into the designated textbox.

**Glycoprotein receptors (Amber path)**

The Amber path additionally offers a *Glycoprotein* receptor type for proteins with covalently attached N- or O-linked glycans. When selected, OpenMMDL Setup:

1. Detects sugar residues by PDB residue name (NAG, NDG, BMA, MAN, FUC, FUL) and finds glycosidic linkages from CONECT records (falling back to a distance scan if absent).
2. Renames residues and atoms to GLYCAM-06j-1 conventions (e.g. NAG → 0YB / 4YB, MAN → 0MA / 3MA / 6MA, with the trimannose branch point as VMB).
3. Emits explicit ``bond`` statements for every protein-glycan and glycan-glycan covalent link, injected into the generated ``tleap.in`` after ``loadpdb``.
4. Sources both the chosen protein force field (e.g. ``leaprc.protein.ff14SB``) and the glycan force field (``leaprc.GLYCAM_06j-1`` by default).

Only the common N-glycan core sugars listed above are currently supported. Unrecognised PDB sugar codes or non-canonical linkage patterns raise a descriptive error; see ``openmmdl/openmmdl_setup/glycoprotein.py`` for the verified GLYCAM tables.