Page Comparison

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Molecule(s) (file(s) + other descriptors such that the organic chemistry is unambiguous)

Force field

Box vectors (implied by file)

Total energy

E_bond

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E_vdW

E_{Electrostatics}

Single ligand: /path/to/ligand0.sdf

openff-1.0.0.offxml

(Implied as none by file) Note that this should not follow the toolkit:

Github link macro

link	https://github.com/openforcefield/openff-toolkit/issues/1084

some number kJ/mol

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Box of organic molecules in liquid phase: /path/to/liquid_box.pdb + a list of SMILES strings for each compound

openff_unconstrained-1.0.0.offxml

(Read from PDB file)

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Protein in vacuo: /path/to/protein.pdb + protein SMILES

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(Read from PDB file)

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Protein in water with ions and a docked ligand: path/to/complex.pdb + protein SMILES + ligand SMILES + SMILES for water and each ion

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(Read from PDB file)

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