Protein-Ligand MD OMM

Upload a prepared protein-ligand complex. Select each noncovalent ligand below, then choose its charge source and structure input. OpenFF Sage 2.3.0 is used for ligand parameters in every charge mode.

Complex structure

Single-model PDB, up to 10 MB. The server verifies ligand chemistry and atom mapping.

Nonstandard residues

Every residue instance is listed separately. Water molecules are hidden; select the noncovalent ligands you want to simulate.

Upload a complex PDB to inspect its residues.

Simulation settings

Job nameProduction length (ns)

Temperature (K)

NaCl concentration (M)

Solvent padding (nm)

Trajectory interval (ps)

Protein: ff14SB · Ligand: OpenFF Sage 2.3.0 · Water: TIP3P · Engine: OpenMM CUDA