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`).

.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Purpose:: Legacy residue definition format similar to .lib; still supported but largely superseded by .lib.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 .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 .prmtop.
Producer → Consumer:: tleap → sander / pmemd

.crd

Format:: Text (coordinate alias)
Purpose:: Legacy coordinate file naming; often synonymous with .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., .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.