Episode 3 - Preparing and editing the system in OpenMM

Table of contents

• Duration
• Objectives
• Content
• Prepare the working folder
• Alanine dipeptide
• Protein-ligand complex
• Key points
• Modeller (OpenMM guide)

Duration

• Session: 60 min
• Exercises: 45 min

Objectives

• Prepare a simple system (alanine) and a complex system (protein-ligand).
• Reproduce the Modeller operations from the OpenMM guide.
• Generate simulation-ready structures and save them reproducibly.

Content

• Simple preparation with Modeller and light solvation.
• PDBFixer to repair complex proteins.
• Modeller: hydrogens, solvent, membranes, extra particles, remove water.
• Example of saving results (Saving the Results).

Prepare the working folder

Before running the scripts, create the root folder where all results will be saved (regardless of where you run the jobs) with course_paths.py:

python docs/episodes/scripts/course_paths.py

This creates the main folder (default ~/Concepcion26), creates data/ and results/, and shows the export COURSE_DIR="..." you must run in the terminal so all scripts use the same destination.

Then copy the data into data/:

cp -R Course-MD-Data-main/* "$COURSE_DIR/data"

Alanine dipeptide

Guided demo

Exercise

• Run the simple script and review "$COURSE_DIR/results/02-preparacion-sistema/simple/alanine_solvated.pdb".

Notebooks and scripts

• This notebook prepares the alanine system with Modeller, adds solvent, and writes the simple solvated PDB ready for simulation. (notebook

  script)

Protein-ligand complex

Guided demo

Exercise

• Run the complex script with --output-dir outputs.
• Try a different --output-base.

Notebooks and scripts

• This notebook walks through Modeller/PDBFixer to repair the protein-ligand complex, allowing you to add solvent, ions, and save preparatory files. (notebook

  script)

Key points

• Preparation depends on the target system.
• Saving prepared versions improves traceability.

Modeller (OpenMM guide)

Add hydrogens

Add solvent

Add membrane

Add extra particles

Remove water

Save results (Saving the Results)

Course script: openmm_modeller_save.py