Quickstart: mlmm scan with -s (YAML spec)

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

  • Optional trajectories when --dump is enabled (scan_trj.xyz, scan.pdb)

Next step