Step 1 / 1_AutomateGromacs.py
System Preparation
Cleans the input structure, handles chains and components, prepares CHARMM-compatible topologies, solvates the system, adds ions, and produces a simulation-ready minimization input.
Why this step matters
MD is unforgiving: a missing atom, ambiguous ligand, wrong chain, or bad topology can invalidate everything downstream. Step 1 turns messy structural input into a reproducible GROMACS system.
Concepts to understand
PDB, CIF, and mmCIF inputs
structure cleanup and hydrogen handling
protein, ligand, cofactor, peptide, RNA, and DNA recognition
CHARMM36 or CHARMM36/LJ-PME topology generation
CGenFF ligand conversion through charmm2gmx
box definition, solvation, ionization, and energy-minimization setup
Common outputs
protein.pdb
protein_processed.gro
complex.gro
solv_ions.gro
topol.top
index.ndx
atomIndex.txt
em.tpr
mdrun.log
Typical commands
python 1_AutomateGromacs.py --pdb CPD32_9G94.pdbpython 1_AutomateGromacs.py --pdb CPD32_9G94.pdb --box-type dodecahedron --box-distance 1.0python 1_AutomateGromacs.py --pdb CPD32_9G94.pdb --strict-pdb-validation