Parmfit Correction

Overview

Correction refines parameters for a molecule that already has a mol2 topology. MAPLE starts from GAFF2 parameters, optionally optimizes the structure and updates bonded terms from a Cartesian Hessian, applies the selected atomic-charge source, optionally refits proper torsions, and exports Amber and GROMACS files. The default chg_fit=none preserves the input mol2 charges; RESP, supported charge-capable MLIPs, and Antechamber charge methods can replace them.

Initial Prepare

The input mol2 must already carry GAFF2 atom types. Users should pre-generate it with a tool such as antechamber -at gaff2 -fi <fmt> -fo mol2 -i <input> -o <output> before running Correction.

Workflow

Initial parameters. Run parmchk2 -s gaff2 -a Y from the input mol2 to build *_original.frcmod.
Optimization and reference. Optimize the structure and prepare the MLIP or optional QM reference geometry required by the enabled refinement stages.
Bonded correction or skip. Use Seminario or modified Seminario to update bond and angle terms, or retain the original terms when bonded=none.
Atomic charges. Preserve the input charges or calculate new charges with RESP, a charge-capable MLIP, or an Antechamber method.
TorsionFit. Scan selected proper torsions and fit the relative profile without changing nonbonded, improper, or topology terms.
Export. Write refined Amber mol2/frcmod and GROMACS top/gro files.

Charge-only operation

If bonded=none and torsionfit=false, MAPLE skips geometry optimization and Hessian evaluation. Charge fitting still runs on the supplied coordinates. chg_fit=none preserves the input mol2 charges and original frcmod; another charge method updates the final mol2 charges while retaining the original atom types and frcmod.

Core Parameters

Parameter	Default	Description
`mol2`	Required	Input topology and atom typing for `method=correction`.
`cmo`	`0 1`	Target molecular charge and multiplicity. If omitted, Correction uses charge/multiplicity already attached to the input structure, falling back to `0 1`.
`bonded`	`mseminario`	Bond/angle update method: `mseminario`, `seminario`, or `none`.
`vib_scale`	`1.0`	Force constant scaling factor for Seminario/mSeminario Hessian-based fitting
`chg_fit`	`none`	Charge source: input mol2 charges, `resp`, a charge-capable MLIP, or a value passed to `antechamber -c`.
`chg_level`	`HF/6-31G(d)`	Gaussian ESP level used only when `chg_fit=resp`.
`chg_route`	Empty	Additional Gaussian route text for RESP ESP jobs.
`iqm`	`false`	Use external QM reference optimization/Hessian and torsion references when enabled. See the main Parmfit page for details.
`torsion_bonds`	Auto	Optional explicit center bonds. Otherwise MAPLE selects rotatable single bonds from the mol2 topology.

For TorsionFit parameters, QM job resources, MLIP optimization controls, and levels of theory, see the TorsionFit, General Settings, and QM Reference sections of the main Parmfit page.

Preserving original GAFF2 parameters

Bond/angle and torsion refinement are controlled separately. Setting bonded=none preserves the original BOND/ANGLE terms; setting torsionfit=false preserves the original DIHE terms. With both disabled, Correction exports the parmchk2/GAFF2 parameters without refinement. When either refinement is enabled, atom types are automatically reassigned (MAPLE Z0/Z1, etc.).

Charge Fitting

chg_fit is independent of iqm. RESP always uses Gaussian and reuses qm_nproc and qm_mem. Correction does not normalize fitted model, RESP, or Antechamber charges; the report prints both the integer target from cmo and the actual sum in the charged mol2 so that any mismatch is visible.

With iqm=true, qm_compare=true, and parameter refinement enabled, charge fitting follows both branch geometries. The primary result uses chargefit/qm_route_charged.mol2, while the MLIP comparison uses chargefit/mlip_route_charged.mol2. For chg_fit=none, the analogous route-specific charged mol2 files are written directly under <base>_work/, and no chargefit/ directory is created.

TorsionFit

Correction auto-selects center bonds from the mol2 topology: proper-torsion central bonds that are single bonds and not in a ring. Use torsion_bonds to provide explicit overrides (e.g. 6-8 12-14). See the main Parmfit page for the two-stage fitting architecture and parameter details.

Input Files

Simple Input

A simple Correction job keeps commonly used Parmfit options in the regular MAPLE input. The inline coordinates provide the working geometry, while the mol2 file supplies topology, atom types, and starting charges.

#model=uma(size=uma-s-1p1,task=omol)
#parmfit(method=correction,mol2=toluene_ff.mol2,cmo=0 1,chg_fit=none,bonded=mseminario,torsionfit=true)
#device=gpu0

C   0.000000  1.520000  0.000000
...

Full External Input

For a longer setup, keep the MAPLE launcher short and move Parmfit parameters into an external .parmfit file. The inline method must match method=correction in the external config. File paths such as mol2 are resolved relative to the .parmfit file.

#model=uma(size=uma-s-1p1,task=omol)
#parmfit(method=correction,input=Correction.parmfit)
#device=gpu0

C   0.000000  1.520000  0.000000
...

Example external Parmfit config

Correction.parmfit

method=correction
mol2=toluene_ff.mol2
cmo=0 1

# QM reference for correction and TorsionFit
iqm=false
qm_engine=g16
opt_level=B3LYP/def2-SVP
sp_level=B3LYP/def2-SVP
opt_route=
sp_route=
qm_mode=1
qm_compare=false
qm_nproc=8
qm_mem=24

# Atomic charges
chg_fit=none
chg_level=HF/6-31G(d)
chg_route=

# Bond/angle correction
bonded=mseminario
vib_scale=1.0

# Geometry optimization LBFGS
memory=5
curvature=70.0
max_step=0.2
max_iter=256
write_traj=false
traj_every=1
verbose=1
use_projection=false
use_line_search=false
bond_constraints=
angle_constraints=
torsion_constraints=

# TorsionFit
torsionfit=true
torsion_bonds=
torsion_steps=36
backend=cgbs
constraint_mode=projected
stage1_weights=true
torsion_refine_rounds=3
torsion_refine_max_iter=256
torsion_refine_tol=1.0e-6
torsion_ensemble=false
torsion_ensemble_ratio=0.3
torsion_ensemble_weight=0.5
report_debug=false

Output Files

<base>_work/<base>_original.frcmod: Initial AmberTools/GAFF2 frcmod from parmchk2.
<base>_work/<base>_maple.mol2: Primary final mol2 with the selected charges; refined workflows use MAPLE atom type naming.
<base>_work/<base>_mlip_maple.mol2: Optional MLIP-comparison mol2 when qm_compare is active.
<base>_work/<base>_maple.frcmod: Refined Amber parameter file.
<base>_work/<base>_maple.top and <base>_work/<base>_maple.gro: GROMACS export for inspection and deployment.
<base>_work/chargefit/{qm_route|mlip_route}_charged.mol2: Route-specific charged mol2 for RESP, charge-capable MLIP, or Antechamber fitting.
<base>_work/{qm_route|mlip_route}_charged.mol2: Charge-preserving work mol2 for chg_fit=none; this mode creates no chargefit/ directory.
<base>_work/torsionfit/: Torsion scan outputs and fit diagnostics.

Requirements and Limits

mSeminario and Seminario update BOND and ANGLE terms only.
TorsionFit changes selected proper torsions only; it does not rewrite topology, nonbonded terms, or impropers.
Automatic center-bond selection follows the input mol2 bond typing. Fix incorrect aromatic, amide, or double-bond labels in the mol2 before fitting.