Parmfit MetalAA

Overview

MetalAA is the parmfit(method=abinitio) route for a PDB target classified as an ion. It locates the target ion and identifies its coordination environment: donor atoms are detected among N, O, S, P, Se, F, Cl, Br, I within donor_cutoff (default 2.7 Å). The target ion together with donor residues and any add_resid entries form the core. Explicit metal-donor SERIAL pairs can be provided via set_bonded to override automatic recognition.

MetalAA then constructs two models. A large model (core + environment residues within cluster_cutoff + span closure) is built for MLIP optimization, RESP charge fitting, and Hessian-based bonded parameterization. Broken peptide boundaries are sealed with ACE/NME caps, and sequence gaps are replaced with Gly bridges to maintain backbone connectivity. A site model (target metal + final core residues only) is the deployable output; RESP charges from the large model are projected onto the site model by original PDB atom serial. In the deployable site model, residue names are shortened to export codes (e.g. CYM becomes CM1, HIS becomes HS1) and atom types are renamed locally: the metal receives M1/M2/..., each direct donor atom receives Y1/Y2/..., while other atoms retain their original forcefield types.

Initial Prepare

The input PDB should carry reasonable protonation states and residue naming. Incorrect assignments will propagate into the large-model charge inference.

Important

Use method=abinitio, not a separate MetalAA method keyword. MAPLE enters this route only when the selected target is recognized as an ion residue in the PDB.

Charge convention (cmo)

The charge in cmo refers to the metal ion plus any non-protein ligands or cofactors—it is not the total system charge. Standard protein residues carry pre-set formal charges that MAPLE automatically adds when inferring the large-model charge:

Residue	ASP	GLU	LYS	ARG	HIP	CYM
Formal charge	-1	-1	+1	+1	+1	-1

The large-model charge is Q_large = cmo_charge + Σ formal_charge(protein residues). The optional third cmo value (oxy) controls the metal formal charge identity (e.g. Fe²⁺ vs Fe³⁺) but does not participate in the total charge.

Correct protein preprocessing is essential: a deprotonated cysteine must be named CYM (charge -1), not CYS (neutral), or the inferred large-model charge will be wrong.

Workflow

Metal-site recognition. Locate the target ion, donor atoms, core residues, and optional user-added residues.
Large model. Build and optimize a large metal-site model for RESP, Hessian, and parameter fitting.
RESP charges. Run Gaussian ESP and RESP, then project charges from the large model to the deployable site model.
Bonded fitting. Use Seminario or modified Seminario to fit metal-related bond and angle terms.
Deployment files. Write site mol2, final metal frcmod, tleap PDB/input, and dry/solvated tleap outputs.

Core Parameters

Parameter	Default	Description
`target`	Required	PDB ion residue selector for the metal center.
`cmo`	`0 1`	`<charge> <multiplicity> [oxidation]`. Oxidation is optional and used for metal identity/formal charge handling.
`cfmol2`	None	One or more cofactor/ligand mol2 templates for nonprotein residues near the metal site.
`add_resid`	None	Additional residues to force into the metal-site core.
`set_bonded`	Auto	Explicit metal-donor serial pairs, written as `SERIAL-SERIAL` tokens.
`cluster_cutoff`	`3.0`	Cutoff in Angstrom for collecting large-model environment residues.
`donor_cutoff`	`2.7`	Cutoff in Angstrom for automatic metal-donor detection.
`chgmod`	`1`	RESP fixed-charge policy for standard backbone atoms.
`fixchg_resids`	None	Residues whose charges should be fixed to standard Amber references during RESP.
`iqm`	`false`	QM reference for geometry optimization and Hessian work. See the main Parmfit page for details.
`chg_level`	`PBE1PBE/def2SVP`	Gaussian level for RESP ESP generation. Always active regardless of `iqm`.
`prom`, `watm`, `ionm`	`ff14SB`, `tip3p`, `12_6`	Protein, water, and ion parameter models for tleap deployment. MetalAA validates `ionm` against `hfe`, `cm`, `iod`, `12_6`, and `12_6_4`.
`bonded`	`mseminario`	Metal-related bond/angle fitting: `mseminario` or `seminario`.
`vib_scale`	`1.0`	Force constant scaling factor for Seminario/mSeminario Hessian-based fitting

For qm_engine, opt_level, QM job resources, and MLIP optimization controls, see the General Settings and QM Reference sections of the main Parmfit page.

RESP Fixed Charges (chgmod)

The chgmod parameter controls which standard backbone atoms are fixed to their Amber reference charges during RESP fitting. Higher values include more atoms in the fixed set:

`chgmod`	Fixed atoms	Description
0	(none)	No automatic backbone fixing; user controls charges through `fixchg_resids`
1	N, CA, C, O, OXT	Fix backbone heavy atoms to Amber reference charges
2	N, H, HA, CA, C, O, OXT	Add amide H and alpha H
3	N, H, HA, CA, CB, C, O, OXT	Add CB (sidechain anchor)

Use fixchg_resids to lock entire residues to standard Amber reference charges regardless of the chgmod policy. Specifying a non-standard residue that lacks a reference charge entry will cause a startup error.

Full Parmfit Input

Checked-in Parmfit config: examples/parmfit/MetalAA.parmfit. Use it from a MAPLE input with #parmfit(method=abinitio,input=MetalAA.parmfit).

MetalAA.parmfit

method=abinitio
target=A462
cmo=-1 6 3

# QM reference
iqm=false
qm_engine=g16
opt_level=PBE1PBE/def2SVP
opt_route=Guess=Read
sp_route=
qm_mode=1
qm_compare=false
qm_nproc=8
qm_mem=24

# RESP charges
resp_backend=gaussian
chg_level=PBE1PBE/def2SVP
chg_route=Guess=Read
chgmod=1
fixchg_resids=

# Force field, water, ion, and bonded fitting
prom=ff14SB
watm=tip3p
ionm=12_6
bonded=mseminario
vib_scale=1.0

# MLIP geometry optimization controls
opt_max_iter=256
opt_max_step=0.2

# Custom cofactor mol2, config-relative path
cfmol2=HEM_ff.mol2

# MetalAA site selection
add_resid=
set_bonded=
cluster_cutoff=3.0
donor_cutoff=2.7

Output Files

<base>_work/<base>_metal_large_raw.pdb and <base>_work/<base>_metal_large_opt.pdb: Large model before and after optimization.
<base>_work/<base>_metal_site_opt.pdb and <base>_work/<base>_metal_site.mol2: Deployable metal-site model.
<base>_work/<base>_metal.frcmod: Final metal/cofactor frcmod file.
<base>_work/<base>_metal_tleap.pdb, <base>_work/<base>_metal_tleap.in, and <base>_work/<base>_metal_tleap.out: tleap deployment and validation files.
<base>_work/<base>_metal_tleap_dry.* and <base>_work/<base>_metal_tleap_solvated.*: dry and solvated topology/coordinate outputs.
<base>_work/metalaa/: Gaussian ESP, RESP, and intermediate charge-fitting files.

Requirements and Limits

Current MetalAA is intended for a single metal center. Another ion inside the donor cutoff is treated as an unsupported case.
Ligand or cofactor residues without reliable atom types should be supplied through cfmol2.
When automatic donor detection is not sufficient, use set_bonded to provide explicit metal-donor serial pairs.