Parmfit Correction

Overview

Correction refines parameters for a molecule that already has a mol2 topology. All atomic charges are taken directly from the user-provided mol2; no RESP fitting is performed. MAPLE starts from GAFF2 parameters, optimizes the structure with the selected calculator, updates bonded terms from a Cartesian Hessian, optionally refits proper torsions, and exports Amber and GROMACS files.

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.
Geometry and Hessian. Optimize the structure, then compute a Cartesian Hessian from MLIP or optional QM reference settings.
Bonded correction. Use Seminario or modified Seminario to update bond and angle force constants/equilibria.
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.

When refinement is skipped

If bonded=none and torsionfit=false, MAPLE skips geometry optimization, Hessian evaluation, and all parameter refinement. The original mol2 and parmchk2-generated frcmod are exported directly.

Core Parameters

Parameter	Default	Description
`mol2`	Required	Input topology and atom typing for `method=correction`.
`bonded`	`mseminario`	Bond/angle update method: `mseminario`, `seminario`, or `none`.
`vib_scale`	`1.0`	Force constant scaling factor for Seminario/mSeminario Hessian-based fitting
`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.).

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.

Full Parmfit Input

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

Correction.parmfit

method=correction
mol2=toluene_ff.mol2

# 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

# 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: Refined mol2 with MAPLE atom type naming.
<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/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.