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

This document provides an overview of common file formats used in AMBER-based
molecular modeling and molecular dynamics workflows. It describes each file’s
format, purpose, and typical producer–consumer relationships within simulation
pipelines.

Overview Table
--------------

The following table summarizes the most commonly encountered file formats.

.. list-table::
   :header-rows: 1
   :widths: 15 18 37 30

   * - File name / extension
     - File type / format
     - Purpose / role
     - Producer → Consumer

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

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

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

   * - ``.prep``
     - Text (AMBER prep format)
     - Legacy residue definition format similar to ``.lib``; still supported
       but largely superseded by ``.lib``.
     - Antechamber / user → ``tleap``

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

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

   * - ``.inpcrd``
     - Text (AMBER coordinate format)
     - Stores initial atomic coordinates and box information for simulations;
       often paired with ``.prmtop``.
     - ``tleap`` → ``sander`` / ``pmemd``

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

   * - ``.rst`` / ``.rst7``
     - Text or binary (AMBER restart)
     - Stores simulation state (coordinates, optionally velocities and box)
       to restart or continue simulations.
     - ``sander`` / ``pmemd`` → ``sander`` / ``pmemd``

   * - ``.mdcrd``
     - Text (AMBER trajectory)
     - Stores time series of atomic coordinates during MD; legacy trajectory
       format.
     - ``sander`` / ``pmemd`` → ``cpptraj``

   * - ``.nc``
     - Binary (NetCDF trajectory)
     - Efficient, portable trajectory format storing coordinates, velocities,
       and/or forces; preferred modern trajectory format.
     - ``sander`` / ``pmemd`` → ``cpptraj``

   * - ``.mdin``
     - Text (AMBER input control)
     - Specifies simulation parameters, run type, restraints, and algorithms
       for MD or minimization.
     - User → ``sander`` / ``pmemd``

   * - ``.mdout``
     - Text (AMBER output log)
     - Records simulation progress, energies, temperatures, and warnings
       for monitoring and diagnostics.
     - ``sander`` / ``pmemd`` → user

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

   * - ``.restrt``
     - Binary (compressed restart)
     - Binary restart format optimized for performance in large simulations.
     - ``pmemd`` → ``pmemd``

   * - ``.top`` / ``.parm7``
     - Text (topology alias)
     - Alternative naming for AMBER topology files, functionally identical
       to ``.prmtop``.
     - ``tleap`` → ``sander`` / ``pmemd``

   * - ``.crd``
     - Text (coordinate alias)
     - Legacy coordinate file naming; often synonymous with ``.inpcrd``.
     - ``tleap`` → ``sander`` / ``pmemd``

   * - ``.cpptraj.in``
     - Text (cpptraj script)
     - Defines analysis operations (RMSD, clustering, free energy
       post-processing) for trajectory analysis.
     - User → ``cpptraj``


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

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