Quickstart: scan

Goal

Drive one or more bond distances from a single structure using a YAML scan specification.

Prerequisites

  • Input structure: pocket.pdb

  • MM topology: real.parm7

  • ML region definition: ml_region.pdb

These are typically generated by mlmm all, mlmm extract, and mlmm mm-parm.

1. Prepare scan.yaml

one_based: true
stages:
 - [[12, 45, 2.20]]
 - [[10, 55, 1.35], [23, 34, 1.80]]

2. Run scan

mlmm scan -i pocket.pdb --parm real.parm7 --model-pdb ml_region.pdb \
 -q 0 -s scan.yaml --print-parsed -o ./result_scan

What to check

  • result_scan/stage_01/result.pdb

  • result_scan/stage_02/result.pdb

  • scan_trj.xyz and scan.pdb (always written)

Inline literal input (without YAML file)

Instead of a YAML spec file, you can pass scan targets directly on the command line:

mlmm scan -i layered.pdb --parm system.parm7 -q 0 \
  --scan-lists "[(1,5,1.4)]" --no-preopt --no-endopt

Or using PDB atom selectors:

mlmm scan -i layered.pdb --parm system.parm7 -q 0 \
  --scan-lists "[('TYR 285 CA','MMT 309 C10',2.20)]" --no-preopt --no-endopt

Both 1-based atom indices and PDB atom name strings are accepted. See scan.md for full details.

For detailed options, run mlmm scan --help-advanced.

Next step