Supporting Information for "ProPrep: (Metallo)protein MD Preparation That Keeps Users Informed and in Control": Replayable Session Logs

Supporting Information: Application Examples ProPrep records every user input during a preparation session to a timestamped log that can be replayed. This deposit contains three such recordings. Replaying one re-runs the entire preparation, answering each prompt with the recorded response, so the preparations described in the manuscript can be reproduced end to end rather than merely inspected. Each archive unpacks to a self-contained directory with its own README giving the exact commands. Example 1 — Lysozyme (PDB 3WL2). A 181-step session covering structure retrieval, redox site detection, filtering, in silico mutagenesis, completeness repair, redox site transformation, protonation state assignment, orientation, topology generation, and MD setup. Includes a reference copy of the output for comparison without re-running. Example 2 — Baloxavir bound to influenza endonuclease (PDB 7K0W, 6FS6). Two linked sessions. The first (230 steps) performs full MCPB parameterization of a dimanganese site with the ligand baloxavir acid, generates a topology, and runs an energy minimization; its parameters are deposited into a local library. The second (129 steps) applies those parameters to a second structure. 7K0W must be replayed before 6FS6. The Gaussian output from the first session is included, since replay reuses it rather than repeating hours of QM. Example 3 — Batch processing of point mutants (PDB 1M1Q). A session template, in which one recorded answer has been promoted to a variable, plus a CSV supplying ten values. ProPrep replays the 189-step workflow once per mutant, writing each to its own directory. Extending the example is a matter of adding rows to the CSV. Structures are fetched from the RCSB PDB during replay, so no coordinate files are included. Requirements: ProPrep 1.15.0