AMBER and Molecular Simulation File Formats

This glossary describes common file formats used in AMBER-based molecular modeling and molecular dynamics workflows. Each entry shows a short title and lists the file’s purpose, the information it contains, its format, what it is produced from, its typical producer–consumer relationship, and how to open it. Terms defined here can be cross-referenced from any other page using the :term: role (for example, :term:`.prmtop`); the Produced from field links to the upstream formats where one exists.

.mol2

Tripos MOL2 file

Purpose:: Describe a small molecule or nonstandard residue for parameterization workflows.
Info contained:: Atom names, atom types, partial charges, bonding, and residue definitions.
Format:: Text (Tripos MOL2).
Produced from:: .pdb or other structure, via external QM / cheminformatics tools or antechamber.
Producer → consumer:: external tools / antechamber → antechamber / parmchk2 / tleap.
Open with:: Text editor; molecular viewer (VMD, Chimera, Avogadro).
Notes:: —

.frcmod

AMBER force-field modification

Purpose:: Supply force-field parameters not present in the standard AMBER force fields.
Info contained:: Missing or custom bond, angle, dihedral, and van der Waals parameters.
Format:: Text (AMBER force-field modification).
Produced from:: .mol2 or .prep, via parmchk2.
Producer → consumer:: antechamber / parmchk2 / user → tleap.
Open with:: Text editor.
Notes:: —

.lib

.off

.prep

AMBER library/object

Purpose:: Define complete residues or molecules for system construction.
Info contained:: Atom names, types, charges, connectivity, and in some cases internal-coordinate residue definitions.
Format:: Text (AMBER residue/library definition).
Produced from:: .mol2 or a structure, via tleap or antechamber.
Producer → consumer:: tleap / antechamber / user → tleap.
Open with:: Text editor.
Notes:: .lib / .off are the standard modern library forms. .prep is a legacy residue-definition format that is still supported but largely superseded by .lib.

_charges.pdb

PDB with partial charges

Purpose:: Human-readable check of partial charges mapped onto atoms.
Info contained:: Atomic coordinates with partial charges in the occupancy/B-factor columns.
Format:: Text (PDB with charges).
Produced from:: .mol2, via antechamber / user.
Producer → consumer:: antechamber / user → visualization tools.
Open with:: Text editor; molecular viewer (VMD).
Notes:: Validation/inspection intermediate; not used directly in production simulations.

.pdb

Protein Data Bank structure

Purpose:: Provide a starting structure for biomolecules or complexes.
Info contained:: Atomic coordinates, residue/atom names, and (sometimes) connectivity.
Format:: Text (Protein Data Bank).
Produced from:: experimental structures (X-ray, NMR, cryo-EM), the Protein Data Bank, or modeling tools.
Producer → consumer:: experimental data / modeling tools → tleap / antechamber.
Open with:: Text editor; molecular viewer (VMD, PyMOL, Chimera).
Notes:: —

.inpcrd

.crd

AMBER input coordinates

Purpose:: Provide the initial coordinates to start a simulation.
Info contained:: Atomic coordinates and box dimensions.
Format:: Text (AMBER coordinate format).
Produced from:: .pdb and force-field libraries, assembled by tleap.
Producer → consumer:: tleap → sander / pmemd.
Open with:: Text editor; VMD (with the matching .prmtop).
Notes:: Historically paired with a topology file such as .parm7. In current practice, .rst7 is the more common standard coordinate/restart file used to start or continue runs. .crd is a legacy naming convention that is often synonymous with .inpcrd.

.parm7

.prmtop

.top

AMBER topology / parameters

Purpose:: Define the complete force-field topology required for every simulation.
Info contained:: Atom types, charges, masses, and all bonded and nonbonded parameters.
Format:: Text (AMBER topology).
Produced from:: force-field libraries (.lib / .off, .frcmod) and a structure, via tleap.
Producer → consumer:: tleap → sander / pmemd / analysis tools.
Open with:: Text editor; parmed; VMD (as a topology).
Notes:: .parm7 is the preferred modern filename in these tutorials. .prmtop and .top are older equivalent names that remain widely supported.

.rst

.rst7

AMBER restart file

Purpose:: Store a simulation state to start from or continue a run.
Info contained:: Coordinates, optionally velocities, and box dimensions.
Format:: Text or binary (AMBER restart).
Produced from:: .inpcrd or a .nc frame; written by sander / pmemd.
Producer → consumer:: tleap / cpptraj / sander / pmemd → sander / pmemd.
Open with:: Text editor (if ASCII); VMD / cpptraj (with the matching .prmtop).
Notes:: Preferred over .mdcrd for storing a single restart state.

.nc

.mdcrd

AMBER trajectory

Purpose:: Store an MD trajectory efficiently and portably.
Info contained:: Per-frame coordinates and, optionally, velocities and/or forces, plus box information.
Format:: Binary NetCDF trajectory or legacy ASCII AMBER trajectory.
Produced from:: an MD run, written by sander / pmemd.
Producer → consumer:: sander / pmemd → cpptraj.
Open with:: cpptraj; VMD (with the matching .prmtop).
Notes:: .nc is the preferred modern trajectory format for performance and portability. .mdcrd is the older legacy text format and is retained mainly for backward compatibility.

.mdin

AMBER run-control input

Purpose:: Control how a minimization or MD run is performed.
Info contained:: Run type, ensemble, restraints, algorithms, and step counts (namelist input).
Format:: Text (AMBER input control).
Produced from:: written by the user (hand-edited or templated).
Producer → consumer:: user → sander / pmemd.
Open with:: Text editor.
Notes:: —

.mdout

AMBER output log

Purpose:: Record run progress and diagnostics for monitoring.
Info contained:: Energies, temperatures, pressures, timings, and warnings per step.
Format:: Text (AMBER output log).
Produced from:: a run, written by sander / pmemd.
Producer → consumer:: sander / pmemd → user / analysis tools.
Open with:: Text editor or pager.
Notes:: —

.en

.mden

AMBER energy output

Purpose:: Provide per-step energy components for post-processing.
Info contained:: Decomposed energy terms over the run.
Format:: Text or binary (energy output).
Produced from:: a run, written by sander / pmemd.
Producer → consumer:: sander / pmemd → analysis tools.
Open with:: Text editor (if ASCII); analysis scripts.
Notes:: .mden is a very common filename for this data stream.

.mdinfo

AMBER run-status summary

Purpose:: Provide a compact progress file that is easy to monitor while a simulation is running.
Info contained:: Step count, time, energies, temperatures, pressure, density, performance, and recent status/warning messages.
Format:: Text (status/progress report).
Produced from:: a run, written by sander / pmemd.
Producer → consumer:: sander / pmemd → user / workflow scripts.
Open with:: Text editor, pager, tail -f.
Notes:: Smaller and easier to watch during a run than .mdout.

.mdfrc

AMBER force trajectory

Purpose:: Store per-frame Cartesian forces for reweighting, machine learning, and specialized post-processing workflows.
Info contained:: Force vectors on each atom for each saved frame.
Format:: Text or binary, depending on program settings.
Produced from:: an MD or analysis run, written by sander / pmemd.
Producer → consumer:: sander / pmemd → analysis tools / ML tools.
Open with:: Analysis scripts and custom post-processing tools.
Notes:: Less common than coordinate trajectories; often paired with .mden and .nc.

.restrt

AMBER binary restart

Purpose:: Store a restart state efficiently for large simulations.
Info contained:: Coordinates, velocities, and box dimensions.
Format:: Binary (compressed restart).
Produced from:: a run, written by pmemd.
Producer → consumer:: pmemd → pmemd.
Open with:: cpptraj; VMD (with the matching .prmtop).
Notes:: Binary restart optimized for performance; see .rst7.

.cpptraj.in

cpptraj analysis script

Purpose:: Script a set of trajectory analysis operations.
Info contained:: cpptraj commands (e.g. trajin/trajout, rms, clustering, free-energy post-processing).
Format:: Text (cpptraj script).
Produced from:: written by the user.
Producer → consumer:: user → cpptraj.
Open with:: Text editor.
Notes:: —

.disang

AMBER NMR-style restraint file

Purpose:: Define distance, angle, torsion, or other restraints applied during a simulation.
Info contained:: &rst namelists describing restrained atoms, target values, force constants, and flat-bottom bounds.
Format:: Text (NMR restraint syntax).
Produced from:: written by the user, templating scripts, or restraint generators.
Producer → consumer:: user / helper scripts → sander / pmemd.
Open with:: Text editor.
Notes:: Common in umbrella sampling, QM/MM reaction-coordinate work, and Boresch-style restraint setups.

.groupfile

Replica/group launch file

Purpose:: Launch multiple AMBER runs together, typically for replica exchange or many-window workflows.
Info contained:: One command line or argument block per replica/window, often including its .mdin, topology, coordinates, and outputs.
Format:: Text (groupfile syntax).
Produced from:: written by the user or workflow-generation scripts.
Producer → consumer:: user / scripts → sander.MPI / pmemd.MPI.
Open with:: Text editor.
Notes:: Widely used for Hamiltonian replica exchange, pKa workflows, and other multi-window alchemical calculations.

.dumpave

AMBER averaged collective-variable output

Purpose:: Save running or windowed averages of restrained variables for monitoring enhanced-sampling or free-energy calculations.
Info contained:: Time series of averaged collective variables or restraint observables.
Format:: Text.
Produced from:: a run using NMR-style restraints or collective variables.
Producer → consumer:: sander / pmemd → user / analysis scripts.
Open with:: Text editor, plotting tools, analysis scripts.
Notes:: Often used alongside .disang files to track umbrella sampling coordinates.

.cv

Collective-variable definition file

Purpose:: Define collective variables and biasing potentials for free-energy or enhanced-sampling workflows.
Info contained:: Variable definitions, atom selections, reference structures, restraints, and bias parameters.
Format:: Text (package-specific collective-variable syntax).
Produced from:: written by the user or generated from templates.
Producer → consumer:: user / scripts → AMBER modules that read Colvars or related CV inputs.
Open with:: Text editor.
Notes:: The exact syntax depends on the collective-variable engine being used.

.dat

General analysis data table

Purpose:: Store numeric data series produced during simulation, post-processing, or plotting workflows.
Info contained:: Columns of values such as energies, dvdl, restraint coordinates, RMSD, free energies, overlaps, or schedule metrics.
Format:: Text table.
Produced from:: analysis programs, conversion scripts, or AMBER tools.
Producer → consumer:: AMBER tools / scripts → plotting tools / analysis scripts / users.
Open with:: Text editor, spreadsheet software, plotting tools.
Notes:: A generic extension; the meaning depends on context. Common examples include efep_*.dat, dvdl_*.dat, and RMSD outputs.

.dcd

DCD trajectory

Purpose:: Store trajectory coordinates in a compact binary format widely supported by visualization tools.
Info contained:: Per-frame atomic coordinates and, depending on the writer, unit-cell information.
Format:: Binary (DCD trajectory).
Produced from:: converted trajectories or runs configured to write DCD via external tools.
Producer → consumer:: analysis/conversion tools → VMD and other viewers.
Open with:: VMD, Chimera, MDAnalysis, other trajectory readers.
Notes:: Often used as a compatibility alternative when a viewer lacks good .nc support on a given platform.

.log

General log file

Purpose:: Record progress, diagnostics, or messages from a workflow, wrapper script, or external program.
Info contained:: Program messages, warnings, errors, command echoing, and sometimes summarized results.
Format:: Text log.
Produced from:: scripts, workflow engines, QM codes, analysis tools, or AMBER-adjacent utilities.
Producer → consumer:: many tools → user / workflow debugging tools.
Open with:: Text editor or pager.
Notes:: Unlike .mdout, this extension is generic and not specific to AMBER.

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.
Run monitoring is often split across .mdout, .mdinfo, and sometimes .mden; together they provide progressively more compact views of the same simulation.
Restrained and enhanced-sampling workflows commonly combine .mdin with .disang, and may also emit .dumpave or other .dat files for the biased coordinates.
Multi-window workflows such as replica exchange, umbrella sampling, and alchemical free-energy calculations often use .groupfile and produce many per-window .rst7, .nc, .mdout, and .dat files.
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.