drug-trajectory-analysis

Goal

To extract quantitative binding-mode descriptors from a protein-ligand MD trajectory, producing:

• Ligand heavy-atom RMSD (pose stability)
• Ligand center-of-mass drift
• Binding-pocket residue RMSF (pocket flexibility)
• Hydrogen bond persistence
• Key contact occupancy
• Protein-ligand interaction fingerprints (IFPs) over time

These outputs feed directly into go/no-go decisions about pose validity and can be used to compare refinement trajectories across compounds.

Instructions

1. Prepare inputs

Required:

• Trajectory: DCD file from drug-protein-ligand-md
• Topology: the solvated complex PDB used as the MD input

2. Run trajectory analysis

# Env: drugmd-agent
python .agents/skills/drug-trajectory-analysis/scripts/analyze_trajectory.py \
  --topology md/system/complex_solvated.pdb \
  --trajectory md/run/production.dcd \
  --ligand_resname UNL \
  --pocket_cutoff 5.0 \
  --output_dir md/analysis/

Key parameters:

• --ligand_resname: residue name of the ligand in the topology (default: UNL). Check the solvated PDB if unsure.
• --pocket_cutoff: distance cutoff in Angstroms for defining pocket residues around the ligand in the first frame (default: 5.0).
• --skip_frames: skip the first N frames as equilibration (default: 0).
• --snapshots: render PyMOL binding pocket snapshots at 4 timepoints (requires pymol-open-source).

3. Output files

The script produces:

• md/analysis/ligand_rmsd.csv: per-frame ligand heavy-atom RMSD (Angstroms)
• md/analysis/ligand_com.csv: per-frame ligand COM relative to protein backbone COM
• md/analysis/pocket_rmsf.csv: per-residue RMSF of pocket residues (Angstroms)
• md/analysis/hbonds.csv: hydrogen bond donor-acceptor pairs and occupancy fractions
• md/analysis/contacts.csv: residue-level contact occupancy fractions
• md/analysis/interaction_fingerprints.csv: per-frame binary IFP matrix (requires ProLIF)
• md/analysis/analysis_summary.json: summary statistics
• md/analysis/plots/: directory with PNG plots (RMSD time series, COM drift, RMSF bar chart, contact occupancy, PyMOL binding pocket snapshots)

4. Interpret results

Key indicators of a stable binding pose:

• Ligand RMSD: should plateau below 2-3 A for a stable pose. Persistent drift above 3 A suggests the ligand is leaving the pocket or adopting an alternative binding mode.
• COM drift: large monotonic drift indicates ligand unbinding.
• Pocket RMSF: identifies flexible vs. rigid pocket regions. High RMSF (>2 A) at key contact residues may indicate induced fit.
• H-bond persistence: critical hydrogen bonds should have >50% occupancy for a well-resolved interaction.
• IFP consistency: stable binding modes show consistent fingerprint patterns across the trajectory.

5. Quick single-metric check

For a fast assessment, check only ligand RMSD:

# Env: drugmd-agent
python .agents/skills/drug-trajectory-analysis/scripts/analyze_trajectory.py \
  --topology md/system/complex_solvated.pdb \
  --trajectory md/run/production.dcd \
  --ligand_resname UNL \
  --rmsd_only \
  --output_dir md/analysis/

Examples

Example: full analysis of TYK2 inhibitor trajectory

# Env: drugmd-agent
python .agents/skills/drug-trajectory-analysis/scripts/analyze_trajectory.py \
  --topology tyk2/md/system/complex_solvated.pdb \
  --trajectory tyk2/md/run/production.dcd \
  --ligand_resname UNL \
  --pocket_cutoff 5.0 \
  --skip_frames 10 \
  --output_dir tyk2/md/analysis/

Constraints

• Environment: Requires drugmd-agent with MDAnalysis and ProLIF.
• Trajectory format: DCD is the default from the MD skill. PDB trajectories and XTC are also supported by MDAnalysis.
• Ligand residue name: must match the name used in the topology PDB. OpenMM often assigns UNL to non-standard residues.
• ProLIF requirement: interaction fingerprints require ProLIF. If ProLIF is not installed, the script skips IFP computation and logs a warning.
• Memory: large trajectories (>10k frames) may require significant memory for IFP computation. Use --skip_frames or --stride to downsample.

References

• Michaud-Agrawal, N.; Denning, E. J.; Woolf, T. B.; Beckstein, O. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 2011, 32, 2319-2327. https://doi.org/10.1002/jcc.21787
• Bouysset, C.; Fiorucci, S. ProLIF: a Library to Encode Molecular Interactions as Fingerprints. J. Cheminform. 2021, 13, 72. https://doi.org/10.1186/s13321-021-00548-6

---

Author: Matthew Cox Contact: GitHub @mcox3406