rst-parameterize-ligand

name	rst-parameterize-ligand
description	Parameterize small-molecule ligands with rust_simulation_tools' built-in antechamber — assign GAFF2 atom types and AM1-BCC or Gasteiger partial charges, write a parameterized mol2, or compute raw AM1 Mulliken charges. Use for "parameterize a ligand", "GAFF2 atom types", "AM1-BCC charges", "antechamber", "Gasteiger charges", or "AM1 charges".

Ligand parameterization (antechamber / AM1-BCC)

Pure-Rust reimplementation of antechamber: GAFF2 atom typing, BCC typing, and AM1-BCC charges (AM1 semi-empirical Mulliken charges + bond-charge corrections), matching AmberTools' sqm to <0.001 e. No external AmberTools install needed.

Standalone: parameterize a ligand file

import rust_simulation_tools as rst

rst.parameterize_ligand(
    input_path="ligand.sdf",        # SDF or mol2 input
    output_path="ligand_gaff2.mol2",# writes GAFF2 types + charges
    net_charge=0,                   # formal charge of the molecule
    charge_method="am1bcc",         # "am1bcc" (accurate) or "gasteiger" (fast)
)

Use am1bcc for production force fields; gasteiger only for quick/approximate charges. The output mol2 carries GAFF2 atom types and per-atom charges ready for SystemBuilder.load_mol2.

Integrated with SystemBuilder

builder.load_ligand("ligand.sdf", net_charge=0) runs this parameterization internally and returns a ready-to-combine System. See rst-build-system.

Raw AM1 Mulliken charges

For advanced use (custom workflows, QM charge analysis), compute AM1 charges directly from atomic numbers and coordinates:

import numpy as np
atomic_numbers = np.array([8, 1, 1], dtype=np.int64)   # water: O, H, H
coords = np.array([
    [0.0,  0.000, 0.000],
    [0.0,  0.757, 0.587],
    [0.0, -0.757, 0.587],
])
charges = rst.compute_am1_charges(atomic_numbers, coords, charge=0)
# charges: ndarray of Mulliken charges, one per atom

Notes:

• atomic_numbers must be int64; coords are Angstroms, shape (N, 3).
• charge is the total molecular charge.
• AM1 uses the NDDO approximation (overlap is identity for same-atom pairs), so Mulliken charge reduces to q = Z - sum(P_diag).

For the equivalent AmberTools commands (antechamber -c bcc -at gaff2, parmchk2), and how to feed a .frcmod/.lib into a build, see rst-build-system. Full example: examples/example_antechamber.py.