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Protein–ligand complex
Use a PDB containing the protein and bound ligand. The system inspects and repairs the structure first, then continues through ligand parameterisation and MD.
Upload complex PDBSelect the workflow by the type of input you have.
Use a PDB containing the protein and bound ligand. The system inspects and repairs the structure first, then continues through ligand parameterisation and MD.
Upload complex PDBUse only when you intentionally want an apo-protein simulation without a ligand.
Open protein-only wizardUse only when the complete GROMACS input has already been prepared and validated elsewhere.
Run prepared input