# parmfitrun.in - resolved parmfit configuration for method=ncaa
# Generated by MAPLE parmfit; values are the user config entries with defaults filled in.
# This file is itself a valid parmfit config and can be referenced via input=.
# residues declared for the NCAA flow (built, then folded or frozen)
ncaa_resids              = HIF89,TRP482
# extra altloc selectors
keep                     = 
# residues force-added to the site
add_resid                = 

# NCAA run
# Non-standard amino acid declaration and residue building
# 1:1 with ncaa_resids
ncaa_charges             = -2,0
# 1:1 with ncaa_resids; keep within 3 characters (PDB limit)
ncaa_resnames            = HF1,WF1
# multiplicity for the NCAA QM jobs
ncaa_mults               = 
# (ff14SB, ff19SB)
pro_ff                   = ff14SB
# (tip3p, spce, tip4pew, opc3, opc, fb3, fb4)
wat_ff                   = tip3p
# (mseminario, seminario, none)
bonded                   = mseminario
# frequency scaling for Seminario constants
vib_scale                = 1.0
# empty = auto-detect (i-j); ';' separates per-residue groups; NCAA: residue-local 1-based (ACE/NME not counted)
torsion_bonds            = 3-8,8-11,6-60,22-25;5-6

# TorsionFit
# Torsion parameter fitting switches and scan controls
torsionfit               = true
# radical centers for improper fitting (!!experimental!!); NCAA: residue-local 1-based (same space as torsion_bonds); Refinement: mol2 serial
radical_center           = 
# refit when parmchk2 penalty exceeds (!!experimental!!)
p_thresh                 = 30.0
# scan points per full torsion rotation
torsion_steps            = 36
# (lbfgs, cgws, cgbs)
backend                  = cgbs
# (fixinternals, projected)
constraint_mode          = projected
torsion_refine_rounds    = 3
torsion_refine_max_iter  = 256
torsion_refine_tol       = 1e-06
stage1_weights           = true
torsion_ensemble         = false
torsion_ensemble_ratio   = 0.3
torsion_ensemble_weight  = 0.5

# QM reference
# QM reference geometry and Hessian jobs
# run QM reference geometry and Hessian jobs
iqm                      = false
# (g16, g09, gaussian, orca)
qm_engine                = g16
# reference optimization level METHOD/BASIS (write it the way the QM engine expects)
opt_level                = B3LYP/def2-SVP
# single-point level; empty = inherit opt_level
sp_level                 = 
# (1=MLIP scan then QM single point per frame, 2=MLIP scan then QM constrained opt per point, 3=projected QM scan with ParmFit optimizer)
qm_mode                  = 1
# extra route keywords appended to the QM route, e.g. SMD(WATER) or GUESS=READ
opt_route                = 
sp_route                 = 
qm_nproc                 = 8
qm_mem                   = 24
# run the MLIP-vs-QM comparison branch
qm_compare               = false

# charge fitting
# Charge fitting method, level and RESP backend
# (none, resp, MLIP models e.g. aimnet2, antechamber methods e.g. abcg2/bcc; defaults to abcg2 when mol2= is auto-generated)
chg_fit                  = resp
# charge level METHOD/BASIS (engine syntax)
chg_level                = HF/6-31G(d)
chg_route                = 
resp_backend             = gaussian

# MLIP optimization
# MLIP geometry optimization controls
opt_max_iter             = 256
# max MLIP optimization step (Angstrom)
opt_max_step             = 0.2