********************************************************************** * * * 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': 'omol'} Task set to 'parmfit' Global parameter: device = gpu0 Parsed configuration: ---------------------------------------- Task: parmfit model : uma(size=uma-s-1p1,task=omol) method : correction input : Refine3.in device : gpu0 Coordinates ********************************************************************** Group 1 (inline) -------------------- 1 I 3.540000 1.420000 0.000000 2 C 3.556000 1.479000 -2.088000 3 C 4.634000 0.906000 -2.762000 4 H 5.455000 0.437000 -2.222000 5 C 4.677000 0.927000 -4.157000 6 H 5.516000 0.480000 -4.682000 7 C 3.641000 1.522000 -4.877000 8 H 3.674000 1.538000 -5.963000 9 C 2.563000 2.095000 -4.204000 10 H 1.760000 2.557000 -4.772000 11 C 2.520000 2.074000 -2.809000 12 O 1.448000 2.645000 -2.189000 13 H 1.536000 2.564000 -1.228000 [Refinement] initial parameter assignment ... ====================================================================== Parmfit Refinement Setup ====================================================================== Input mol2: choi001_gaff2.mol2 Initial frcmod: Refine3_work/Refine3_original.frcmod Topology atoms: 13 Topology bonds: 13 Bonded refinement: mSeminario QM reference: enabled, mode=2, engine=g16, opt=B3LYP/def2SVP, sp=B3LYP/def2SVP QM compare: disabled TorsionFit: enabled Torsion backend: cgbs Torsion constraint:projected Torsion ensemble:false Scan grid: 10.0000 deg x 36 steps Stage2 refine: max_fast_cycles=3, max_iter_per_cycle=256, tol=1e-06 Torsion bonds: auto-select non-ring torsion bonds with proper torsions Assigned terms: bonds: 13 (unmatched: 0) angles: 19 (unmatched: 0) dihedrals: 26 (unmatched: 0) impropers: 6 (unmatched: 0) nonbonds: 13 (unmatched: 0) ====================================================================== [Refinement] MLIP geometry optimization ... [Refinement] QM reference optimization ... [Refinement] QM Hessian + mSeminario ... ============================================================================================================ mSeminario bond/angle changes ============================================================================================================ Display convention: left = before this stage | right = after this stage Only changed force-field items are shown below. ------------------------------------------------------------------------------------------------------------ BONDS ------------------------------------------------------------------------------------------------------------ (1,2) i-ca k=107.060000 r=2.157000 | k=104.642314 r=2.133670 (2,3) ca-ca k=354.250000 r=1.399000 | k=385.263216 r=1.397583 (2,11) ca-ca k=354.250000 r=1.399000 | k=345.546315 r=1.407974 (3,4) ca-ha k=360.690000 r=1.086000 | k=384.753274 r=1.091535 (3,5) ca-ca k=354.250000 r=1.399000 | k=400.494768 r=1.396059 (5,6) ca-ha k=360.690000 r=1.086000 | k=382.550481 r=1.092128 (5,7) ca-ca k=354.250000 r=1.399000 | k=395.215940 r=1.399901 (7,8) ca-ha k=360.690000 r=1.086000 | k=381.098338 r=1.092785 (7,9) ca-ca k=354.250000 r=1.399000 | k=421.051938 r=1.392170 (9,10) ca-ha k=360.690000 r=1.086000 | k=383.800093 r=1.092050 (9,11) ca-ca k=354.250000 r=1.399000 | k=361.976590 r=1.406146 (11,12) ca-oh k=348.550000 r=1.364000 | k=386.754755 r=1.347493 (12,13) oh-ho k=535.510000 r=0.973000 | k=533.717733 r=0.972078 ------------------------------------------------------------------------------------------------------------ ANGLES ------------------------------------------------------------------------------------------------------------ (1,2,3) i-ca-ca k=58.260000 theta=119.1700 | k=43.566640 theta=119.9258 (1,2,11) i-ca-ca k=58.260000 theta=119.1700 | k=43.550471 theta=118.7861 (3,2,11) ca-ca-ca k=63.670000 theta=120.0200 | k=88.465813 theta=121.2881 (2,3,4) ca-ca-ha k=44.900000 theta=119.8800 | k=29.181829 theta=119.8704 (2,3,5) ca-ca-ca k=63.670000 theta=120.0200 | k=81.273692 theta=119.8219 (4,3,5) ha-ca-ca k=44.900000 theta=119.8800 | k=31.026336 theta=120.3076 (3,5,6) ca-ca-ha k=44.900000 theta=119.8800 | k=32.060641 theta=119.7623 (3,5,7) ca-ca-ca k=63.670000 theta=120.0200 | k=98.589117 theta=119.5270 (6,5,7) ha-ca-ca k=44.900000 theta=119.8800 | k=31.974068 theta=120.7107 (5,7,8) ca-ca-ha k=44.900000 theta=119.8800 | k=32.787125 theta=120.0844 (5,7,9) ca-ca-ca k=63.670000 theta=120.0200 | k=97.439177 theta=120.5350 (8,7,9) ha-ca-ca k=44.900000 theta=119.8800 | k=32.675911 theta=119.3806 (7,9,10) ca-ca-ha k=44.900000 theta=119.8800 | k=32.619503 theta=121.6141 (7,9,11) ca-ca-ca k=63.670000 theta=120.0200 | k=91.229139 theta=120.7841 (10,9,11) ha-ca-ca k=44.900000 theta=119.8800 | k=32.070753 theta=117.6018 (2,11,9) ca-ca-ca k=63.670000 theta=120.0200 | k=103.816019 theta=118.0438 (2,11,12) ca-ca-oh k=78.860000 theta=119.9000 | k=77.994569 theta=124.2001 (9,11,12) ca-ca-oh k=78.860000 theta=119.9000 | k=86.504942 theta=117.7561 (11,12,13) ca-oh-ho k=67.410000 theta=108.5800 | k=69.115387 theta=109.4735 [Refinement] atomic charge fitting ... [Refinement] TorsionFit ... [Refinement] Using QM reference data for TorsionFit (mode=2) ... ============================================================================================================ TorsionFit torsion changes ============================================================================================================ Display convention: left = before this stage | right = after this stage Only changed force-field items are shown below. ------------------------------------------------------------------------------------------------------------ DIHEDRALS ------------------------------------------------------------------------------------------------------------ (2,11,12,13) ca-ca-oh-ho term=1 k=0.855000 n=2.000 phase=180.0000 | k=1.289158 n=2.000 phase=-179.9838 (2,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=0.583821 n=1.000 phase=0.0417 (2,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.046609 n=3.000 phase=-0.2318 (2,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.014970 n=4.000 phase=179.9530 (9,11,12,13) ca-ca-oh-ho term=1 k=0.855000 n=2.000 phase=180.0000 | k=1.137656 n=2.000 phase=-179.9863 (9,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=0.600379 n=1.000 phase=-179.9608 (9,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.077415 n=3.000 phase=179.8671 (9,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.029978 n=4.000 phase=179.9164 [Refinement] export GROMACS ... [Refinement] export Amber ... ====================================================================== PARMFIT REFINEMENT RESULT ====================================================================== Status: completed Input mol2: choi001_gaff2.mol2 Main products: Amber mol2: Refine3_work/Refine3_maple.mol2 Amber frcmod: Refine3_work/Refine3_maple.frcmod GROMACS top: Refine3_work/Refine3_maple.top GROMACS gro: Refine3_work/Refine3_maple.gro Amber tleap: Refine3_work/Refine3_maple_tleap.in Charge fitting: method: resp RESP level: HF/def2SVP target charge: 0 actual charge: -0.00000000 work MOL2: Refine3_work/chargefit/qm_route_charged.mol2 final MOL2: Refine3_work/Refine3_maple.mol2 Stage timing: TorsionFit 26m 14s Hessian + mSeminario 1m 17s charge fitting 4s geometry optimization 2s initial parameter assignment 0s export Amber 0s export GROMACS 0s Parameter changes: bonded refinement: mSeminario bonds changed by bonded refine: 13 angles changed by bonded refine: 19 dihedrals changed by TorsionFit: 2 other changes: none Torsion energy trace: torsion bond (11, 12): scan xyz: Refine3_work/torsionfit/Refine3_qm_torsionfit_11-12_scan_final.xyz angle_deg QM_ref orig_ref stage0_ref stage1_ref stage2_ref 359.9837 0.000000 0.000000 0.000000 0.000000 0.000000 369.9837 0.166791 0.126529 0.147141 0.161604 0.164693 379.9837 0.649320 0.496473 0.574809 0.630328 0.641784 389.9837 1.393270 1.074265 1.242780 1.357634 1.380266 399.9837 2.320095 1.802067 2.090049 2.270265 2.303513 409.9837 3.332954 2.600877 3.036366 3.273992 3.314008 419.9837 4.328439 3.393744 3.996144 4.269699 4.310410 429.9837 5.208085 4.099577 4.882896 5.159183 5.194093 439.9837 5.886486 4.651587 5.617998 5.853498 5.877625 449.9837 6.298577 5.005032 6.143340 6.283574 6.294680 459.9837 6.409116 5.144998 6.436135 6.413445 6.411813 469.9837 6.225129 5.091351 6.513367 6.247826 6.234743 479.9837 5.791188 4.888763 6.421598 5.829399 5.805428 489.9837 5.181384 4.596496 6.221099 5.231146 5.195466 499.9837 4.484231 4.272484 5.970356 4.544292 4.495375 509.9837 3.797119 3.967687 5.720032 3.869159 3.806206 519.9837 3.216981 3.722949 5.511511 3.303972 3.228223 529.9837 2.828944 3.565987 5.375069 2.930140 2.845352 539.9837 2.692331 3.512102 5.327857 2.799482 2.711410 549.9837 2.828059 3.565604 5.375025 2.929312 2.844468 559.9837 3.215340 3.722146 5.511571 3.302466 3.226611 569.9837 3.794971 3.966659 5.720224 3.867019 3.803923 579.9837 4.481880 4.271460 5.970957 4.541873 4.492790 589.9837 5.179149 4.596010 6.222595 5.229122 5.193273 599.9837 5.789395 4.889544 6.423946 5.827986 5.803858 609.9837 6.224036 5.092263 6.516173 6.246977 6.233762 619.9837 6.408928 5.146943 6.439408 6.413444 6.411708 629.9837 6.299387 5.007783 6.147036 6.284664 6.295693 639.9837 5.888224 4.655511 5.621936 5.855694 5.879763 649.9837 5.210605 4.104207 4.886559 5.162038 5.196899 659.9837 4.331485 3.398053 3.998614 4.272205 4.312867 669.9837 3.336238 2.606491 3.039213 3.277551 3.317521 679.9837 2.323286 1.806171 2.092268 2.273593 2.306800 689.9837 1.396027 1.077298 1.244401 1.360450 1.383048 699.9837 0.651372 0.497339 0.575808 0.632310 0.643738 709.9837 0.167926 0.124229 0.147551 0.162563 0.165637 719.9837 0.000065 -0.003831 -0.000469 -0.000469 -0.000469 QM_ref vs stage2_final: MAE = 0.010873 kcal/mol, RMSE = 0.012221 kcal/mol TorsionFit: state: enabled torsion bonds: (11, 12) scan files: (11, 12): Refine3_work/torsionfit/Refine3_qm_torsionfit_11-12_scan_final.xyz stage1: completed stage2: enabled, max_fast_cycles=3 fast cycles: executed=2, accepted=1, rejected=1 final parameters: Stage2 fast cycle 1 Warnings: none ====================================================================== ====================================================================== IMPORTANT ====================================================================== Due to the limitations of custom atom types, the exported topology must be normalized with ParmEd before use. tleap identifies hydrogens by the leading character of the atom type, which MAPLE types do not carry, so it writes an empty BONDS_INC_HYDROGEN section and SHAKE (ntc=2) would constrain nothing. ParmEd rebuilds that section from ATOMIC_NUMBER, e.g.: tleap -f Refine3_maple_tleap.in parmed -p Refine3_maple_gas.prmtop <<< $'outparm Refine3_maple_gas_parmed.prmtop\nquit' ====================================================================== Program started: 2026-10-03 06:03:17 ====================================================================== TIMING SUMMARY ====================================================================== Input Reading....................................... 1.153 s ( 0.1 %) Settings Parsing.................................... 1.151 s ( 99.8 %) Coordinate Section Parsing.......................... 0.001 s ( 0.1 %) Post-Processing Expansion........................... 0.000 s ( 0.0 %) MLP Initialization.................................. 12.409 s ( 0.7 %) Job Dispatching..................................... 1656.999 s ( 99.2 %) Parmfit optimization................................ 1656.997 s ( 100.0 %) Parmfit correction.................................. 1656.906 s ( 100.0 %) ====================================================================== Total wall time: 1670.561 s Total CPU time: 39.944 s ====================================================================== Program ended: 2026-10-03 06:31:08 TOTAL RUN TIME: 0 days 0 hours 27 minutes 50 seconds 560 msec