Parmfit NCAA

Overview

NCAA is the parmfit(method=abinitio) route for a noncanonical amino acid residue classified as a protein residue. It builds capped ACE-target-NME models, where the backbone and caps are frozen during optimization so that only the sidechain R-group relaxes. Atomic charges are obtained through RESP, a charge-capable MLIP, or an Antechamber method; AmberTools prepin/frcmod templates are then created, and bond/angle terms plus sidechain torsions are refined. Deployment is validated with tleap.

Target

target must identify exactly one protein residue in the input PDB. Use a chain and residue number such as A123, include an insertion code when present (A123A), or use a residue name and number such as HIF123. A selector without a chain must still be unique. The selected residue must contain the peptide backbone atoms required by NCAA; rn controls only the output residue name and does not affect target selection.

Workflow

1. Target identity. Locate the target residue and detect backbone, sidechain anchor, and chirality.
2. Capped models. Build and optimize α and β ACE-target-NME conformers.
3. Atomic charges. Fit the optimized conformers with the configured chg_fit route and prepare the charged capped mol2.
4. AmberTools template. Use the fitted charges with antechamber, prepgen, and parmchk2 to create the initial prepin/frcmod files.
5. Parameter refinement. Apply Seminario/mSeminario to bond/angle terms and TorsionFit to target-residue sidechain torsions.
6. Deployment. Write refined prepin/frcmod, processed protein PDB, tleap input, and tleap validation outputs.

Core Parameters

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.

Charge Fitting

NCAA fits the optimized α and β capped conformers. With chg_fit=resp, Gaussian ESP data from both conformers enter one joint two-stage RESP fit. A charge-capable MLIP or Antechamber method evaluates the two conformers separately, after which MAPLE applies their equal-weight per-atom average. For model and Antechamber routes, a final backbone adjustment closes the target-residue charge in the prepin to the cmo value.

chg_fit is independent of iqm. RESP always uses Gaussian with chg_level, chg_route, qm_nproc, and qm_mem. NCAA cannot use chg_fit=none because a PDB input does not supply a reusable set of atomic charges.

All charge-route files remain under <base>_work/ncaa/. The resulting charged capped mol2 and target.chg feed the prepin/GAFF2 template build; the same charges are carried into the Stage 0 parameter set and the TorsionFit baseline.

TorsionFit

NCAA uses a center-bond filter that restricts torsion fitting to target-residue sidechain torsions only; backbone–backbone and cap torsion bonds are excluded. For residues with particularly complex sidechains, consider setting torsionfit=false and relying on the original GAFF2 torsion parameters, or use torsion_bonds to refine specific dihedrals selectively. NCAA disables torsion ensemble targets internally; see the main Parmfit page for scan and refinement parameter details.

Peptide Boundary Terms

When the NCAA residue is inserted as a custom template, MAPLE dynamically generates ProteinFF-GAFF2 cross-terms at both peptide boundaries: the head side (prev_C–target_N) and the tail side (target_C–next_N). These include exact BOND, ANGLE, and DIHE terms that connect the custom template atom types to the neighbouring standard protein residue atom types.

Input Files

Simple Input

A simple NCAA job keeps commonly used route options in the regular MAPLE input. The target selects the noncanonical protein residue, and the PDB block supplies the complete structure.

#model=uma(size=uma-s-1p1)
#parmfit(method=abinitio,target=A123,rn=MOL,cmo=0 1,chg_fit=resp,bonded=mseminario,torsionfit=false)
#device=gpu0

PDB ncaa.pdb

Full External Input

For a longer setup, keep the MAPLE launcher short and move Parmfit parameters into an external .parmfit file. The launcher and external config must both use method=abinitio. The PDB remains in the MAPLE input; do not place pdb, input, or global MAPLE options in the external config.

#model=uma(size=uma-s-1p1)
#parmfit(method=abinitio,input=NCAA.parmfit)
#device=gpu0

PDB ncaa.pdb

Example external Parmfit config

method=abinitio
target=A123
cmo=0 1

# QM reference
iqm=false
qm_engine=g16
opt_level=B3LYP/def2-SVP
sp_level=B3LYP/def2-SVP
opt_route=em=gd3bj
sp_route=
qm_mode=1
qm_compare=false
qm_nproc=8
qm_mem=24

# Atomic charges
chg_fit=resp
resp_backend=gaussian
chg_level=HF/6-31G(d)
chg_route=

# Residue, force field, water, ion, and bonded fitting
rn=MOL
prom=ff14SB
watm=tip3p
ionm=hfe
bonded=mseminario
vib_scale=1.0

# NCAA capped-conformer optimization controls
opt_max_iter=256
opt_max_step=0.2

# TorsionFit
torsionfit=false
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/<rn>.prepin and <base>_work/<rn>.frcmod: Initial AmberTools residue template files.
• <base>_work/<rn>_maple.prepin and <base>_work/<rn>_maple.frcmod: Refined MAPLE residue template and parameter files.
• <base>_work/<base>_ncaa_tleap.pdb and <base>_work/<base>_ncaa_tleap.in: Processed protein PDB and tleap input.
• <base>_work/<base>_ncaa.prmtop, <base>_work/<base>_ncaa.inpcrd, and solvated PDB outputs: tleap validation products.
• <base>_work/ncaa/: Optimized conformers, charge-route files, charged capped mol2, target.chg, AmberTools template intermediates, and torsion-refinement data.

Requirements and Limits

• The target must be a protein residue with enough backbone and sidechain identity for capping and chirality detection.
• chg_fit=none is unsupported because NCAA has no input mol2 charges to preserve.
• When selected, RESP uses the Gaussian backend; model and Antechamber charge routes do not require RESP.
• The final target-residue charge written for model and Antechamber methods is constrained to the cmo charge.
• TorsionFit is restricted to target-residue sidechain-related center bonds and does not fit peptide backbone torsions.