Episode 1 - Introduction (environment and data)

Table of contents

• Duration
• Objectives
• Content
• Preliminary sequence and ligand checks
• Alanine dipeptide
• Protein-ligand complex
• Key points

Duration

• Session: 45 min
• Exercises: 30 min

Objectives

• Identify input files for alanine and the protein-ligand complex.
• Verify OpenMM and OpenFF Toolkit work in the environment.
• Load base data for both systems following the first-steps workflow.

Content

• PDB and MOL/SDF as inputs.
• Reading alanine with OpenMM.
• Reading protein and ligand with OpenFF Toolkit.
• Working path COURSE_DIR and environment validation.

Preliminary sequence and ligand checks

Before we launch the OpenMM demos, review two focused notebooks to explore the inputs.

• Sequence exploration: <a href="/Curso-MD-Analisis/episodes/notebooks/01-introduction-sequence-check.ipynb">01-introduction-sequence-check.ipynb</a> now focuses on the protein2-ligand2.pdb coordinates and extracts the amino-acid sequence for the two chains before the simulation steps.
• Ligand exploration: <a href="/Curso-MD-Analisis/episodes/notebooks/01-introduction-ligand-check.ipynb">01-introduction-ligand-check.ipynb</a> explores the new $COURSE_DIR/data/complex/ligand2.sdf entry with RDKit, reports its properties, and sketches the ligand before combining it with OpenMM.

Alanine dipeptide

Guided demo

Exercise

• Run the simple script and confirm atom counts.

Notebooks and scripts

• Recorrer esta versión guiada del episodio muestra la estructura del directorio COURSE_DIR, explica cómo leer un PDB con Biopython y prepara el sistema de alanina para el flujo de trabajo básico. (notebook

  script)

Protein-ligand complex

Visual sanity checks

• Open $COURSE_DIR/data/complex/protein2-ligand2.pdb with the new <a href="/Curso-MD-Analisis/episodes/notebooks/01-introduccion-protein2-nglview.ipynb">complex viewer</a> to inspect the binding pose with nglview.
• Slice the same structure with bash docs/episodes/scripts/01-split-protein2-ligand2.sh and check the standalone protein in <a href="/Curso-MD-Analisis/episodes/notebooks/01-introduccion-protein2-protein-nglview.ipynb">protein viewer</a> as well as the ligand in <a href="/Curso-MD-Analisis/episodes/notebooks/01-introduccion-protein2-ligand-nglview.ipynb">ligand viewer</a>.
• These quick viewers keep you aligned with the complex before the OpenMM preparation steps and complement the protein/ligand notebooks listed above.

Splitting the complex

Recreate the canonical protein2.pdb / ligand2.pdb pair any time the $COURSE_DIR/data/complex folder changes by running the helper script below (copy/paste from the repository). It assumes the full complex resides in $COURSE_DIR/data/complex/protein2-ligand2.pdb:

#!/usr/bin/env bash
set -euo pipefail

COURSE_DIR="${COURSE_DIR:-$HOME/Concepcion26}"
INPUT_PATH="$COURSE_DIR/data/complex/protein2-ligand2.pdb"
OUTPUT_DIR="$COURSE_DIR/data/complex"

if [[ ! -f "$INPUT_PATH" ]]; then
  echo "Error: missing $INPUT_PATH" >&2
  exit 1
fi

mkdir -p "$OUTPUT_DIR"

python - <<PY
from pathlib import Path

input_path = Path("$INPUT_PATH")
output_dir = Path("$OUTPUT_DIR")
protein_path = output_dir / "protein2.pdb"
ligand_path = output_dir / "ligand2.pdb"

protein_lines = []
ligand_lines = []

with input_path.open("r") as fh:
    for line in fh:
        if line.startswith("HETATM") and line[17:20].strip() == "SUB":
            ligand_lines.append(line)
        else:
            protein_lines.append(line)

protein_path.write_text("".join(protein_lines))
ligand_path.write_text("".join(ligand_lines))

print(f"Saved protein {protein_path}")
print(f"Saved ligand  {ligand_path}")
PY

Run this once after updating the data bundle so every episode reads the same split files.

Guided demo

Exercise

• Run the complex script and swap the ligand for ligand1.sdf.
• Save the output to a text file.

Notebooks and scripts

• Esta versión completa repasa la preparación del complejo proteína-ligando: secuencia rápida con Biopython, visualización con nglview y escritura de archivos Amber para la simulación. (notebook

  script)

• The new nglview viewers keep the same split seen above but in interactive form: complex viewer, protein viewer, and ligand viewer.

Key points

• The course works with a simple and a complex system in parallel.
• OpenMM and OpenFF Toolkit cover reading PDB and MOL/SDF.