Pipeline

Pipeline stages and what each script does

The PyMACS scripts are numbered because each one answers a different scientific and operational need.

Step 1: setup

Script 1 cleans the input structure, detects chains and retained components, prepares CHARMM-compatible topologies, converts CGenFF ligand files when needed, defines the simulation box, solvates, adds ions, and creates the energy-minimization input.

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python 1_AutomateGromacs.py --pdb complex.pdb --ligand LIG

Step 2: EM, NVT, NPT, and production

Script 2 runs the physics stages in order: energy minimization, temperature equilibration, pressure/density equilibration, and production MD. It also handles CPU/GPU choices and checkpoint-safe continuation.

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python 2_AutomateGromacs.py --mode ligand --ligand LIG --ns 1 --compute auto

Step 3A: trajectory analysis

Script 3A turns raw trajectories into interpretable outputs: centered final trajectories, RMSD, RMSF, radius of gyration, secondary-structure summaries, ligand contacts, interaction-type tables, and mode-specific analyses.

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python 3A_AutomateGromacs.py --mode ligand --ligand LIG --headless

Step 3B and 3C: networks

Step 3B renders ligand-centered or peptide-contact networks. Step 3C handles protein-protein and protein-peptide interface residue interaction networks.

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python 3B_NETWORX.py --ligand LIG
python 3C_Interface_RIN.py --contact-cutoff 4.0 --min-contact-frac 0.10

Step 4: figurebook

Step 4 packages generated figures into a PDF figurebook for review, sharing, and manuscript preparation.

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python 4PDF4MD.py