manual_ligands.md

Manual Ligand Input Contract

SIMPLE supports manual parameter input for custom residues and small molecules when you do not want to run antechamber and parmchk2.

Accepted file bundles

• mol2 + frcmod
• prepi + frcmod
• off + frcmod
• lib + frcmod

Required information

Your manual files must encode:

• Amber atom types for every atom
• Partial charges for every atom
• Bond connectivity
• Residue and atom names that are consistent with the cleaned PDB loaded into tleap

Notes

• mol2 is expected to include atom types and charges.
• prepi or off/lib defines the residue template used by tleap.
• frcmod must contain any missing bonded or Lennard-Jones parameters not already covered by the selected force field.
• If you provide only a partial bundle, SIMPLE will stop before tleap execution and print the missing requirements.