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