Docking preparation

Status: notebook-based, manual preparation; incomplete as an end-to-end pipeline. There is no automated HADDOCK submission, validated enzyme–polymer complex builder, or catalytic-activity predictor in this workflow.

1. Choose the polymer structure

Both enzyme workflows (05B → 06B and 05A → 06C) start from a docked enzyme–PHA complex PDB. Notebook 11 reads the polymer benchmark folder that notebook 10 writes, examples/output/benchmark/<system>/gromacs/solvated_polymer/, by default its final structure step7_production.gro (GRO_NAME; step5_input.gro is the structure before MD). Review that path and confirm the intended system and structure. The benchmark needs actual generated input files; the package does not distribute completed benchmark trajectories.

2. Prepare and inspect the PDB

The notebook writes the polymer only (residue POLYMER_RESNAME: PHA for 06A systems, LIG for CHARMM-GUI systems) to examples/output/docking_inputs/<system>/, with iphasimulator.docking_inputs.export_polymer_pdb(). Before writing it checks that the polymer is whole: every bonded heavy-atom pair (bonds from the topology) must be shorter than 0.3 nm. If not, it stops; use a whole-molecule frame instead, such as the representative frame from notebook 08 or gmx trjconv -pbc mol.

Inspect chain/residue identifiers, atom names, elements and terminal groups in the exported PDB. Elements come from the topology masses (or the atom names); atoms and residues are renumbered from 1 in chain A, and no box record is written.

3. Prepare the enzyme separately

Supply the reviewed enzyme structure and decide the docking restraints for the specific research question. The enzyme annotations and binding statements in the historical notebook are user-supplied context, not independently validated results of this package. Confirm them against your own evidence before use.

4. Record the manual docking job

Upload inputs through your chosen docking service when ready, and retain the input files, restraints, job identifiers and returned results. The notebook provides preparation notes and records; it does not submit the job.

For an existing MD trajectory of a complex, use contact analysis to examine proximity. Contact occupancy cannot establish affinity or catalytic activity.

Notebook: 11 docking preparation.