**********************************************************************
*                                                                    *
*                        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          : NCAA1.in
device         : gpu0

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

Group 1 (PDB File)
Resolved PDB: /home/hungn/Desktop/MyRepo/MLP/parmfit_tutorial/NCAA/Case1/MaDA.pdb
PDB coordinates are parsed by the parmfit route at runtime.
--------------------

======================================================================
                             Parmfit NCAA                             
======================================================================
Target: _89:HIF (protein)
  PDB residue templates: matched=516, backbone_only=1, unmatched=0
    non-standard (matched backbone only): _89:HIF (target)
    template overrides (renamed): _10:CYM (CYX->CYM), _74:CYM (CYX->CYM)
  PDB target charge: _89:HIF = -2 (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 skipped ...
  [NCAA] writing refined templates + tleap input ...
  [NCAA] tleap validation ...
  [NCAA] route completed; final summary follows.

======================================================================
                         PARMFIT NCAA RESULT                          
======================================================================
Status: completed
Route: NCAA
Target: _89:HIF
Residue name: HF1
Chirality: L
Protein ff: ff14SB
Res charge/spin-multi: -2 1
Charge fitting: resp
Charge level: HF/6-31G(d)
Target charge: -2
Actual charge: -2.00000000
Charge MOL2: NCAA1_work/ncaa/HIF89/NCAA1_capped.mol2

Main products:
  refined prepin: NCAA1_work/HF1_maple.prepin
  refined frcmod: NCAA1_work/HF1_maple.frcmod
  tleap PDB:      NCAA1_work/NCAA1_ncaa_tleap.pdb
  tleap input:    NCAA1_work/NCAA1_ncaa_tleap.in

Stage timing:
  charge fitting                    7m 46s
  Hessian + mSeminario              1m 30s
  model preparation + reference        49s
  tleap validation                     11s
  AmberTools template build             0s
  final export                          0s

Next step:
  cd NCAA1_work
  tleap -s -f NCAA1_ncaa_tleap.in |tee NCAA1_ncaa_tleap.out

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

Warnings:
  none
======================================================================



Program started: 2026-10-09 06:58:34

======================================================================
                      TIMING SUMMARY
======================================================================
Input Reading.......................................   1.156 s  (   0.2 %)
  Settings Parsing....................................   1.144 s  (  98.9 %)
  Coordinate Section Parsing..........................   0.001 s  (   0.1 %)
  Post-Processing Expansion...........................   0.000 s  (   0.0 %)
MLP Initialization..................................  12.006 s  (   1.9 %)
Job Dispatching..................................... 619.163 s  (  97.9 %)
  Parmfit optimization................................ 619.161 s  ( 100.0 %)
    Parmfit NCAA........................................ 619.058 s  ( 100.0 %)
======================================================================
Total wall time: 632.325 s
Total CPU time: 157.245 s
======================================================================

Program ended: 2026-10-09 07:09:06
TOTAL RUN TIME: 0 days 0 hours 10 minutes 32 seconds 324 msec