********************************************************************** * * * 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 : Refine2.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: Refine2_work/Refine2_original.frcmod Topology atoms: 13 Topology bonds: 13 Bonded refinement: mSeminario QM reference: enabled, mode=1, 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=104.642308 r=2.133670 (2,3) ca-ca k=354.250000 r=1.399000 | k=385.263234 r=1.397583 (2,11) ca-ca k=354.250000 r=1.399000 | k=345.546300 r=1.407974 (3,4) ca-ha k=360.690000 r=1.086000 | k=384.753278 r=1.091535 (3,5) ca-ca k=354.250000 r=1.399000 | k=400.494741 r=1.396059 (5,6) ca-ha k=360.690000 r=1.086000 | k=382.550486 r=1.092128 (5,7) ca-ca k=354.250000 r=1.399000 | k=395.215958 r=1.399901 (7,8) ca-ha k=360.690000 r=1.086000 | k=381.098334 r=1.092785 (7,9) ca-ca k=354.250000 r=1.399000 | k=421.051929 r=1.392170 (9,10) ca-ha k=360.690000 r=1.086000 | k=383.800091 r=1.092050 (9,11) ca-ca k=354.250000 r=1.399000 | k=361.976614 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=533.717737 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=29.181827 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=31.026334 theta=120.3076 (3,5,6) ca-ca-ha k=44.900000 theta=119.8800 | k=32.060643 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=31.974069 theta=120.7107 (5,7,8) ca-ca-ha k=44.900000 theta=119.8800 | k=32.787127 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=32.675914 theta=119.3806 (7,9,10) ca-ca-ha k=44.900000 theta=119.8800 | k=32.619506 theta=121.6141 (7,9,11) ca-ca-ca k=63.670000 theta=120.0200 | k=91.229140 theta=120.7841 (10,9,11) ha-ca-ca k=44.900000 theta=119.8800 | k=32.070756 theta=117.6018 (2,11,9) ca-ca-ca k=63.670000 theta=120.0200 | k=103.816018 theta=118.0438 (2,11,12) ca-ca-oh k=78.860000 theta=119.9000 | k=77.994570 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=69.115392 theta=109.4735 [Refinement] atomic charge fitting ... [Refinement] TorsionFit ... [Refinement] Using QM reference data for TorsionFit (mode=1) ... ============================================================================================================ 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=1.103279 n=2.000 phase=-179.6053 (2,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=0.177444 n=1.000 phase=8.4237 (2,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.004840 n=3.000 phase=-117.3981 (2,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.035436 n=4.000 phase=-174.8265 (9,11,12,13) ca-ca-oh-ho term=1 k=0.855000 n=2.000 phase=180.0000 | k=1.101867 n=2.000 phase=-179.7300 (9,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=0.177649 n=1.000 phase=-171.5662 (9,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.004091 n=3.000 phase=62.9473 (9,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.034934 n=4.000 phase=-175.1832 [Refinement] export GROMACS ... [Refinement] export Amber ... ====================================================================== PARMFIT REFINEMENT RESULT ====================================================================== Status: completed Input mol2: choi001_gaff2.mol2 Main products: Amber mol2: Refine2_work/Refine2_maple.mol2 Amber frcmod: Refine2_work/Refine2_maple.frcmod GROMACS top: Refine2_work/Refine2_maple.top GROMACS gro: Refine2_work/Refine2_maple.gro Amber tleap: Refine2_work/Refine2_maple_tleap.in Charge fitting: method: resp RESP level: HF/def2SVP target charge: 0 actual charge: -0.00000000 work MOL2: Refine2_work/chargefit/qm_route_charged.mol2 final MOL2: Refine2_work/Refine2_maple.mol2 Stage timing: TorsionFit 5m 23s Hessian + mSeminario 1m 29s 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: Refine2_work/torsionfit/Refine2_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 0.208213 0.148268 0.159940 0.197624 0.197976 379.9837 0.773613 0.549843 0.599973 0.750227 0.750787 389.9837 1.623683 1.167627 1.280879 1.590847 1.591518 399.9837 2.676070 1.958648 2.173365 2.652391 2.653102 409.9837 3.758558 2.814591 3.102093 3.725003 3.725625 419.9837 4.814268 3.689148 4.081832 4.800522 4.800737 429.9837 5.712598 4.471635 4.942360 5.702491 5.701691 439.9837 6.382778 5.081806 5.595642 6.349123 6.346372 449.9837 6.797966 5.510018 6.071056 6.780848 6.774974 459.9837 6.924858 5.703398 6.272680 6.909315 6.899083 469.9837 6.783636 5.690196 6.252329 6.786152 6.770499 479.9837 6.418118 5.498156 6.032260 6.427735 6.405982 489.9837 5.885994 5.182918 5.677908 5.894883 5.866851 499.9837 5.266240 4.816676 5.276891 5.280560 5.246586 509.9837 4.647613 4.467243 4.897647 4.673710 4.634559 519.9837 4.120151 4.186091 4.589618 4.157361 4.114081 529.9837 3.761179 4.004898 4.397576 3.814261 3.768054 539.9837 3.637952 3.943321 4.334225 3.687777 3.639927 549.9837 3.759507 4.003591 4.408983 3.800102 3.751953 559.9837 4.109704 4.179572 4.619954 4.139610 4.092571 569.9837 4.632877 4.452651 4.945617 4.655894 4.611406 579.9837 5.248548 4.788967 5.345487 5.270368 5.229815 589.9837 5.871572 5.141468 5.784566 5.912980 5.877536 599.9837 6.405850 5.439962 6.131613 6.430286 6.400736 609.9837 6.786682 5.630317 6.376997 6.806138 6.782732 619.9837 6.946920 5.647555 6.412335 6.937460 6.919869 629.9837 6.845170 5.459432 6.225452 6.820834 6.808236 639.9837 6.445528 5.044603 5.777436 6.420989 6.412275 649.9837 5.797704 4.437839 5.126940 5.791047 5.785056 659.9837 4.929086 3.669183 4.289860 4.935138 4.930897 669.9837 3.885367 2.797473 3.297735 3.874427 3.871278 679.9837 2.800828 1.936223 2.322681 2.781573 2.779181 689.9837 1.777433 1.163988 1.442447 1.751236 1.749494 699.9837 0.951914 0.553694 0.764204 0.922349 0.921245 709.9837 0.369465 0.171150 0.289380 0.334082 0.333583 719.9837 0.177670 0.039683 0.138105 0.138087 0.138091 QM_ref vs stage2_final: MAE = 0.018492 kcal/mol, RMSE = 0.021605 kcal/mol TorsionFit: state: enabled torsion bonds: (11, 12) scan files: (11, 12): Refine2_work/torsionfit/Refine2_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 Refine2_maple_tleap.in parmed -p Refine2_maple_gas.prmtop <<< $'outparm Refine2_maple_gas_parmed.prmtop\nquit' ====================================================================== Program started: 2026-10-02 23:58:38 ====================================================================== TIMING SUMMARY ====================================================================== Input Reading....................................... 0.020 s ( 0.0 %) Settings Parsing.................................... 0.018 s ( 89.8 %) Coordinate Section Parsing.......................... 0.000 s ( 2.2 %) Post-Processing Expansion........................... 0.000 s ( 0.0 %) MLP Initialization.................................. 12.868 s ( 3.0 %) Job Dispatching..................................... 418.121 s ( 97.0 %) Parmfit optimization................................ 418.119 s ( 100.0 %) Parmfit correction.................................. 418.060 s ( 100.0 %) ====================================================================== Total wall time: 431.009 s Total CPU time: 37.983 s ====================================================================== Program ended: 2026-10-03 00:05:49 TOTAL RUN TIME: 0 days 0 hours 7 minutes 11 seconds 9 msec