Output Directory Layout

This page lists the main files that the commands write, the default output directories, and where each file goes inside all. Each command page lists all of its files under Output files.

Filename conventions

Filename

Written by

Purpose

summary.json

all and path-search

The aggregate JSON result (see JSON Output Reference).

summary.json

per-stage and report commands with --out-json (default --no-out-json)

A copy of the command’s result.json; the two files are identical when the write completes. mm-parm, define-layer, fix-altloc, add-elem-info, bond-summary, oniom-export, and oniom-import do not write it.

result.json

With --out-json: opt, tsopt, freq, irc, sp, scan / scan2d / scan3d, path-opt, dft, extract, trj2fig, energy-diagram

The JSON result of one command or report, also written when the run ends without converging. extract, trj2fig, and energy-diagram write it next to their first output file.

run.log

CLI and Colab runs, once the output directory exists

The command line (quoted for the shell) and the stdout/stderr printed while the command runs, including the lines that show how the run ended; the command’s page lists them (for example opt → Checking convergence). Help, version, and dry-run calls do not create it, nor do the commands without an output directory (extract, mm-parm, define-layer, add-elem-info, fix-altloc, bond-summary, trj2fig, energy-diagram, oniom-export, oniom-import).

summary.log

path-search, all

Text summary. The header gives Scientific status; the numbered sections give the barrier and bond changes of each segment and the output tree (see all → Reading the run status).

final_geometry.xyz / final_geometry.pdb

opt, tsopt

Optimized geometry, the structure to pass to the next command; also written when the optimization does not converge. The .xyz is always written; the .pdb is for PDB/mmCIF input and carries the layers in its B-factors.

mep_trj.pdb / mep_trj.cif / mep_trj.xyz

path-search

Reaction path frames. The .cif is added for mmCIF or large-PDB input when file conversion is on.

final_geometries_trj.xyz / hei.xyz

path-opt

Reaction path frames (all images) and the highest-energy image (HEI). When file conversion is on, .pdb copies (final_geometries.pdb, hei.pdb) are added, plus .cif copies for mmCIF or large-PDB input.

mep_plot.png / energy_diagram_MEP.png

path-search

Energy profile of the minimum energy path (MEP): mep_plot.png along the path, energy_diagram_MEP.png as a state-energy diagram. all places both at its root.

finished_irc_trj.xyz / forward_irc_trj.xyz / backward_irc_trj.xyz

irc

IRC (intrinsic reaction coordinate) trajectories (full path plus each branch), with a .pdb copy when a reference topology is available and a .cif copy for mmCIF or large-PDB input.

forward_first.xyz / backward_last.xyz

irc

Ends of the two branches: the endpoint candidates to optimize with opt.

frequencies_cm-1.txt

freq

Vibrational mode listing.

ml_region_without_linkH.xyz / ml_region_with_linkH.xyz

dft

The ML region without and with the link hydrogens, as the DFT calculation sees it; .pdb copies are written for PDB input. Inside all, they are in each segments/seg_NN/dft/{R,TS,P}/.

*.pdb / *.cif

commands with --convert-files (the default; --no-convert-files turns it off), and extract

Copies of the outputs in the input format, written next to them: PDB for PDB/mmCIF input, plus a .cif that keeps the original chain IDs, residue numbers, and insertion codes for mmCIF or large-PDB input. A multi-frame trajectory becomes a multi-model CIF. extract has no toggle and always writes the .cif for mmCIF or large-PDB input.

Default --out-dir

Subcommand

Default --out-dir

all

./result_all/

opt

./result_opt/

tsopt

./result_tsopt/

freq

./result_freq/

irc

./result_irc/

dft

./result_dft/

scan

./result_scan/

scan2d

./result_scan2d/

scan3d

./result_scan3d/

path-opt

./result_path_opt/

path-search

./result_path_search/

sp

./result_sp/

extract

./ (writes pocket.pdb, or pocket_<input>.pdb for multiple inputs)

mm-parm

./ (writes <prefix>.parm7 and <prefix>.rst7; the prefix defaults to the input file name without .pdb)

define-layer

next to the input file (writes <input>_layered.pdb)

Set another directory with -o/--out-dir <path>. The preparation commands take file paths instead: extract takes one or more -o/--output <file> paths, mm-parm an -o/--out-prefix <prefix>, and define-layer an -o/--output <file>.

Standalone vs all

A standalone subcommand writes a flat result_<subcmd>/ directory, without segments/ or _work/. Inside all, each post-processing stage uses the same file layout under segments/seg_NN/ in ts/, irc/, freq/, and dft/.

  • path-search / path-opt are laid out differently. Run standalone, they write the files in the table above to result_path_search/ or result_path_opt/. Inside all, the MEP search runs path-opt by default and the recursive path-search with --refine-path; the raw output stays in _work/path_opt/ or _work/path_search/, and only the MEP files (mep_trj.*, mep_plot.png, energy_diagram_MEP.png) are moved to the root.

The all tree has three parts: the deliverables at the root, segments/, and _work/. The tree below shows the main entries; all → Output files lists every file, including those inside seg_NN/, and the names of the energy diagrams:

result_all/
├─ summary.log · summary.json                        # run summary
├─ mep_trj.pdb · mep_trj.cif · mep_trj.xyz           # MEP coordinates
├─ mep_plot.png · energy_diagram_MEP.png · energy_diagram_*_all.png · irc_plot_all.png
├─ ml_region.pdb                                     # ML region (reusable with --model-pdb)
├─ mm_parm/                                          # Amber topology <input>.parm7 / .rst7 (reusable with --parm7)
├─ layered/                                          # full structures with the layers in the B-factors
├─ segments/
│  └─ seg_NN/                                        # one reaction step: seg_01, seg_02, ...
│     ├─ reactant.{pdb,cif,xyz} · ts.* · product.*   # optimized R, TS, and P (--tsopt)
│     └─ ts/ · irc/ · endpoint_opt/ · freq/{R,TS,P}/ · dft/{R,TS,P}/  # per-stage working files (--tsopt / --thermo / --dft)
└─ _work/                                            # intermediate files, including the TS candidates (HEI)
   ├─ pockets/ · scan/
   └─ path_opt/                                      # MEP search and hei_seg_NN.* (path_search/ with --refine-path)

In TS-only mode (one transition-state (TS) candidate given with --tsopt and no -s/--scan-lists) there is no MEP stage, so _work/path_opt/ is absent and the deliverables live under segments/seg_01/.

Notes

  • Runs that stop early: a run that stops at the argument or input checks, before its output directory is set up, may write none of the files above.

  • summary.json / result.json without --out-json: a successful per-stage run writes them only with --out-json. When a run stops on an exception after the output directory is set up, both are written even without the flag, with "execution_status": "failed" and an "error_type".

  • --no-convert-files in all: it cannot be combined with --tsopt, --thermo, or --dft.

See Also