**********************************************************************
*                                                                    *
*                        M   A   P   L   E                           *
*                                                                    *
*      MAchine-learning Potential for Landscape Exploration          *
*                                                                    *
*                                                                    *
*      © 2025 University of Pittsburgh. All rights reserved.         *
*      Licensed under CC BY 4.0 for academic use.                    *
*                                                                    *
*      Principal Developer:  Xujian Wang                             *
*                                                                    *
**********************************************************************


Parsing # commands...
Global parameter: model = uma with options {'size': 'uma-s-1p1'}
Task set to 'parmfit'
Global parameter: device = gpu0
Parsed configuration:
----------------------------------------
Task: parmfit
model          : uma(size=uma-s-1p1)
method         : ncaa
input          : NCAA3.in
device         : gpu0

                             Coordinates                              
**********************************************************************

Group 1 (PDB File)
Resolved PDB: /home/hungn/Desktop/MyRepo/MLP/parmfit_tutorial/NCAA/Case3/MaDA.pdb
PDB coordinates are parsed by the parmfit route at runtime.
--------------------

======================================================================
                             Parmfit NCAA                             
======================================================================
Target: _89:HIF, _482:TRP (protein)
  PDB residue templates: matched=516, backbone_only=1, unmatched=0
    non-standard (matched backbone only): _89:HIF (also note)
    template overrides (renamed): _10:CYM (CYX->CYM), _74:CYM (CYX->CYM)
  PDB target charges: _89:HIF = -2, _482:TRP = 0 (from your input)
  [NCAA] MLIP model preparation + reference optimization ...
  NCAA target selector: HIF89
  residue name: HF1
  chirality: L
  net charge / spin multiplicity: -2 1
  protein ff: ff14SB
  bonded refinement: mseminario
  charge fitting: resp
  charge level: HF/6-31G(d)
  [NCAA] atomic charge fitting (resp) ...
  [NCAA] AmberTools template build ...
  [NCAA] MLIP Hessian + mSeminario ...
  [NCAA] TorsionFit ...
  [NCAA] writing refined templates + tleap input ...
  [NCAA] route completed; final summary follows.
  [NCAA] MLIP model preparation + reference optimization ...
  NCAA target selector: TRP482
  residue name: WF1
  chirality: L
  net charge / spin multiplicity: 0 1
  protein ff: ff14SB
  bonded refinement: mseminario
  charge fitting: resp
  charge level: HF/6-31G(d)
  [NCAA] atomic charge fitting (resp) ...
  [NCAA] AmberTools template build ...
  [NCAA] MLIP Hessian + mSeminario ...
  [NCAA] TorsionFit ...
  [NCAA] writing refined templates + tleap input ...
  [NCAA] route completed; final summary follows.
  [NCAA] tleap validation ...

======================================================================
                         PARMFIT NCAA RESULT                          
======================================================================
Status: completed
Route: NCAA
Target: _482:TRP
Residue name: WF1
Chirality: L
Protein ff: ff14SB
Res charge/spin-multi: 0 1
Charge fitting: resp
Charge level: HF/6-31G(d)
Target charge: 0
Actual charge: 0.00000100
Charge MOL2: NCAA3_work/ncaa/TRP482/NCAA3_capped.mol2

Main products:
  refined prepin: NCAA3_work/WF1_maple.prepin
  refined frcmod: NCAA3_work/WF1_maple.frcmod
  tleap PDB:      NCAA3_work/NCAA3_ncaa_tleap.pdb
  tleap input:    NCAA3_work/NCAA3_ncaa_tleap.in

Stage timing:
  charge fitting                       31s
  Hessian + mSeminario                 13s
  model preparation + reference        11s
  TorsionFit                            1s
  AmberTools template build             0s
  final export                          0s

Next step:
  cd NCAA3_work
  tleap -s -f NCAA3_ncaa_tleap.in |tee NCAA3_ncaa_tleap.out

Tleap status:
  Errors: 0
  Warnings: 3
  Notes: 0

Warnings:
  none
======================================================================
  NCAA residues built: _89:HIF -> HF1, _482:TRP -> WF1



Program started: 2026-10-09 09:14:32

======================================================================
                      TIMING SUMMARY
======================================================================
Input Reading.......................................   1.150 s  (   0.0 %)
  Settings Parsing....................................   1.149 s  (  99.9 %)
  Coordinate Section Parsing..........................   0.001 s  (   0.1 %)
  Post-Processing Expansion...........................   0.000 s  (   0.0 %)
MLP Initialization..................................  11.704 s  (   0.2 %)
Job Dispatching..................................... 6042.766 s  (  99.8 %)
  Parmfit optimization................................ 6042.764 s  ( 100.0 %)
    Parmfit NCAA........................................ 6042.698 s  ( 100.0 %)
======================================================================
Total wall time: 6055.620 s
Total CPU time: 5648.107 s
======================================================================

Program ended: 2026-10-09 10:55:28
TOTAL RUN TIME: 0 days 1 hours 40 minutes 55 seconds 620 msec