Quickstart: pdb2reaction all (Endpoint mode)

Goal

Run the end-to-end workflow once from two full PDB structures.

Prerequisites

  • pdb2reaction installed (see Installation)

  • Two PDB/mmCIF files (reactant R and product P) with hydrogen atoms already added

  • The same atom identities in the same order across all reaction-ordered input files

About the example filenames: 1.R.pdb and 3.P.pdb mirror the numbered reactant/product files shipped in the geranyl pyrophosphate (GPP) C6-methyltransferase BezA example directory (examples/ — 1.R.pdb = reactant state, 3.P.pdb = product state, with intermediate 2.*.pdb files for multi-step runs). Replace them with the two (or more) full-system PDBs for your own reaction. To run the commands below verbatim, first fetch the bundled example: git clone https://github.com/t-0hmura/pdb2reaction && cd pdb2reaction/examples.

Minimal command

pdb2reaction all -i 1.R.pdb 3.P.pdb -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' \
 --out-dir ./result_all

(Optional) Add post-processing in the same run

pdb2reaction all -i 1.R.pdb 3.P.pdb -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' \
 --tsopt --thermo --dft --out-dir ./result_all

VRAM warning: --dft launches GPU4PySCF single-point jobs on the extracted cluster. Memory use depends on the structure, basis, functional, precision, and software stack; pilot a representative state and monitor peak memory on the target node. On OOM, run pdb2reaction dft separately with a smaller basis / trimmed cluster or use a larger node. The [dft] extra must also be installed (see Installation Step 7).

Expected output

A successful run produces a directory like:

result_all/
├── summary.log                    # Human-readable summary
├── summary.json                   # Machine-readable results
├── mep.pdb                        # Concatenated MEP path (promoted to the root)
├── energy_diagram_MEP.png         # All-segment MEP energy profile
└── _work/                         # Pipeline scratch (safe to delete)
    └── path_opt/                  # Raw MEP-engine output (path_search/ with --refine-path)
        ├── hei_seg_01.{xyz,pdb}   # Highest-energy MEP image
        └── summary.json           # MEP engine results

The minimal command stops after the MEP stage and therefore does not create segments/. With --tsopt, a successfully validated reactive segment adds segments/seg_01/{reactant.pdb,ts.pdb,product.pdb}, ts/, and irc/; adding --thermo also adds freq/.

Output validation

  1. summary.json — use scientific_status and scientific_status_reasons for usability. In path mode, segments[].barrier_kcal is the raw MEP electronic barrier; requested post-processing results are reported under rate_limiting_step and post_segments. status is retained for compatibility.

  2. _work/path_opt/hei_seg_01.pdb — inspect the highest-energy image; with --tsopt, also inspect the canonical segments/seg_01/*.pdb R/TS/P structures

  3. energy_diagram_*.png — the energy profile should show a clear barrier

Sample terminal output (successful run):

[time] Elapsed Time for Whole Pipeline: HH:MM:SS.sss

(Wall-clock varies with system size, GPU, and selected stages.)

If --tsopt is enabled, you should also see:

[Imaginary modes] n=1 ([-425.9])

A first-order saddle point shows exactly one imaginary mode along the reaction coordinate. IRC validation (run automatically as part of --tsopt) confirms it connects the expected reactant and product.

Tips

  • pdb2reaction all --help shows core options; pdb2reaction all --help-advanced shows the full list.

Next step