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.

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Legacy residue definition format similar to .lib; still supported but largely superseded by .lib.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.