Molecular Structure Checking

Check and repair a PDB entry before MD: model/chain selection, alternate locations, disulfides, amides, chirality, missing side chains and backbone (Modeller), then a short AMBER minimization and a final quality report.

by Temple Compute

Run Molecular Structure Checking on Horus

W-23 · Molecular Structure Checking

Domain: BioExcel Building Blocks

Overview

Checks and repairs a raw PDB entry before MD (default: human adenylate kinase 1A with AP5A, PDB 1Z83). It selects a model and chain, resolves alternate locations and disulfides, strips metals, ligands, waters and hydrogens, fixes amides and chirality, models missing side-chain and backbone atoms (Modeller), minimizes with sander, and writes a final quality report. The workflow has 20 tasks.

Pipeline

fetch_pdb -> structure_check                  Download, initial quality report
extract_model -> extract_chain                Model 1, selected chain
fix_altlocs -> fix_ssbonds                    Alternate locations, disulfides (CYX)
remove_molecules_metals / _ligands            Remove listed metal ions and ligands
reduce_remove_hydrogens -> remove_pdb_water   Strip hydrogens and waters
fix_amides -> fix_chirality -> fix_side_chain
canonical_fasta -> fix_backbone               Missing backbone via Modeller
leap_gen_top -> sander_mdrun -> amber_to_pdb  AMBER topology, minimization
fix_pdb -> structure_check_final              Renumber, final quality report

Inputs / Outputs

Outputs (results/):

downloaded.pdb, report.json: raw structure and initial report
models.pdb, chains.pdb, altloc.pdb, ssbonds.pdb, metals.pdb, ligands.pdb, hydrogens.pdb, water.pdb, amides.pdb, chiral.pdb, sidechains.pdb: one structure per repair step
canonical.fasta, backbone.pdb: canonical sequence and backbone-completed structure
amber.pdb, amber.top, amber.crd, trj.*, amber_min.pdb: AMBER topology, coordinates and minimization output
final.pdb, report_final.json: final structure and quality report

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 1z83 | PDB code to check and repair. | | chain | A | Chain to keep. | | altlocs | ["A45:A","A67:A","A85:A"] | JSON list of alternate-location picks, one per residue (chain, residue, altloc kept); [] skips the step. Default is for 1Z83. | | remove_metals | ZN | Comma-separated metal ion residue names to strip; empty keeps all. Fails if none is present. | | remove_ligands | SO4,AP5 | Comma-separated ligand residue names to strip; empty keeps all. Fails if none is present. | | minimization_steps | 500 | sander minimization cycles (0-20000). |