AMBER and Molecular Simulation File Formats
===========================================

This glossary describes common file formats used in AMBER-based molecular
modeling and molecular dynamics workflows. Each entry lists the file's format,
its purpose, and its typical producer–consumer relationship within simulation
pipelines. Terms defined here can be cross-referenced from any other page using
the ``:term:`` role (for example, ``:term:`.prmtop```).

.. glossary::

   .mol2
      :Format: Text (Tripos MOL2)
      :Purpose: Stores atom types, bonding, residue definitions, and partial
         charges for small molecules or nonstandard residues; primary input for
         parameterization workflows.
      :Producer → Consumer: External QM tools / Antechamber → Antechamber, ``tleap``

   .frcmod
      :Format: Text (AMBER force-field modification)
      :Purpose: Provides missing or custom force-field parameters (bond, angle,
         dihedral, van der Waals) not present in standard AMBER force fields.
      :Producer → Consumer: Antechamber / ``parmchk2`` / user → ``tleap``

   .lib
   .off
      :Format: Text (AMBER library/object)
      :Purpose: Defines complete residues or molecules including atom names,
         types, charges, and connectivity for system construction.
      :Producer → Consumer: ``tleap`` / user → ``tleap``

   .prep
      :Format: Text (AMBER prep format)
      :Purpose: Legacy residue definition format similar to :term:`.lib`; still
         supported but largely superseded by :term:`.lib`.
      :Producer → Consumer: Antechamber / user → ``tleap``

   _charges.pdb
      :Format: Text (PDB with charges)
      :Purpose: Human-readable mapping of partial charges onto atomic
         coordinates for validation, inspection, or visualization.
      :Producer → Consumer: Antechamber / user → visualization tools

   .pdb
      :Format: Text (Protein Data Bank)
      :Purpose: Stores atomic coordinates and connectivity for biomolecules or
         complexes; often used as starting structural input.
      :Producer → Consumer: Experimental data / modeling tools → ``tleap``

   .inpcrd
      :Format: Text (AMBER coordinate format)
      :Purpose: Stores initial atomic coordinates and box information for
         simulations; often paired with :term:`.prmtop`.
      :Producer → Consumer: ``tleap`` → ``sander`` / ``pmemd``

   .prmtop
      :Format: Text (AMBER topology)
      :Purpose: Contains complete force-field topology: atom types, charges,
         bonded and nonbonded parameters; essential for all simulations.
      :Producer → Consumer: ``tleap`` → ``sander`` / ``pmemd`` / analysis tools

   .rst
   .rst7
      :Format: Text or binary (AMBER restart)
      :Purpose: Stores simulation state (coordinates, optionally velocities and
         box) to restart or continue simulations.
      :Producer → Consumer: ``sander`` / ``pmemd`` → ``sander`` / ``pmemd``

   .mdcrd
      :Format: Text (AMBER trajectory)
      :Purpose: Stores time series of atomic coordinates during MD; legacy
         trajectory format.
      :Producer → Consumer: ``sander`` / ``pmemd`` → ``cpptraj``

   .nc
      :Format: Binary (NetCDF trajectory)
      :Purpose: Efficient, portable trajectory format storing coordinates,
         velocities, and/or forces; preferred modern trajectory format.
      :Producer → Consumer: ``sander`` / ``pmemd`` → ``cpptraj``

   .mdin
      :Format: Text (AMBER input control)
      :Purpose: Specifies simulation parameters, run type, restraints, and
         algorithms for MD or minimization.
      :Producer → Consumer: User → ``sander`` / ``pmemd``

   .mdout
      :Format: Text (AMBER output log)
      :Purpose: Records simulation progress, energies, temperatures, and
         warnings for monitoring and diagnostics.
      :Producer → Consumer: ``sander`` / ``pmemd`` → user

   .en
      :Format: Text or binary (energy output)
      :Purpose: Stores per-step energy components for post-processing and
         analysis.
      :Producer → Consumer: ``sander`` / ``pmemd`` → analysis tools

   .restrt
      :Format: Binary (compressed restart)
      :Purpose: Binary restart format optimized for performance in large
         simulations.
      :Producer → Consumer: ``pmemd`` → ``pmemd``

   .top
   .parm7
      :Format: Text (topology alias)
      :Purpose: Alternative naming for AMBER topology files, functionally
         identical to :term:`.prmtop`.
      :Producer → Consumer: ``tleap`` → ``sander`` / ``pmemd``

   .crd
      :Format: Text (coordinate alias)
      :Purpose: Legacy coordinate file naming; often synonymous with
         :term:`.inpcrd`.
      :Producer → Consumer: ``tleap`` → ``sander`` / ``pmemd``

   .cpptraj.in
      :Format: Text (cpptraj script)
      :Purpose: Defines analysis operations (RMSD, clustering, free energy
         post-processing) for trajectory analysis.
      :Producer → Consumer: User → ``cpptraj``


Notes on Usage
--------------

* **Topology + coordinates** are always required together for simulations
  (e.g., :term:`.prmtop` + :term:`.inpcrd` or :term:`.rst7`).
* **NetCDF** (:term:`.nc`) trajectories are strongly recommended over legacy
  :term:`.mdcrd` for performance and portability.
* Legacy formats such as :term:`.prep` and :term:`.crd` are retained mainly for
  backward compatibility.
* Human-readable intermediates (e.g., :term:`_charges.pdb`) are useful for
  validation but are not used directly in production simulations.