********************************************************************** * * * 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 : Refine4.in : True level : tight 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: Refine4_work/Refine4_original.frcmod Topology atoms: 13 Topology bonds: 13 Bonded refinement: mSeminario QM reference: enabled, mode=3, 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=104.673921 r=2.133625 (2,3) ca-ca k=354.250000 r=1.399000 | k=385.096562 r=1.397652 (2,11) ca-ca k=354.250000 r=1.399000 | k=345.685929 r=1.407913 (3,4) ca-ha k=360.690000 r=1.086000 | k=384.738820 r=1.091539 (3,5) ca-ca k=354.250000 r=1.399000 | k=400.661509 r=1.395994 (5,6) ca-ha k=360.690000 r=1.086000 | k=382.546623 r=1.092131 (5,7) ca-ca k=354.250000 r=1.399000 | k=395.046163 r=1.399969 (7,8) ca-ha k=360.690000 r=1.086000 | k=381.097482 r=1.092785 (7,9) ca-ca k=354.250000 r=1.399000 | k=421.234418 r=1.392102 (9,10) ca-ha k=360.690000 r=1.086000 | k=383.798242 r=1.092052 (9,11) ca-ca k=354.250000 r=1.399000 | k=361.751164 r=1.406240 (11,12) ca-oh k=348.550000 r=1.364000 | k=386.784376 r=1.347483 (12,13) oh-ho k=535.510000 r=0.973000 | k=533.705122 r=0.972081 ------------------------------------------------------------------------------------------------------------ ANGLES ------------------------------------------------------------------------------------------------------------ (1,2,3) i-ca-ca k=58.260000 theta=119.1700 | k=43.564284 theta=119.9274 (1,2,11) i-ca-ca k=58.260000 theta=119.1700 | k=43.543383 theta=118.7880 (3,2,11) ca-ca-ca k=63.670000 theta=120.0200 | k=88.464009 theta=121.2846 (2,3,4) ca-ca-ha k=44.900000 theta=119.8800 | k=29.183828 theta=119.8685 (2,3,5) ca-ca-ca k=63.670000 theta=120.0200 | k=81.277534 theta=119.8230 (4,3,5) ha-ca-ca k=44.900000 theta=119.8800 | k=31.025598 theta=120.3085 (3,5,6) ca-ca-ha k=44.900000 theta=119.8800 | k=32.059821 theta=119.7632 (3,5,7) ca-ca-ca k=63.670000 theta=120.0200 | k=98.589820 theta=119.5286 (6,5,7) ha-ca-ca k=44.900000 theta=119.8800 | k=31.975590 theta=120.7081 (5,7,8) ca-ca-ha k=44.900000 theta=119.8800 | k=32.787454 theta=120.0774 (5,7,9) ca-ca-ca k=63.670000 theta=120.0200 | k=97.436510 theta=120.5344 (8,7,9) ha-ca-ca k=44.900000 theta=119.8800 | k=32.673611 theta=119.3882 (7,9,10) ca-ca-ha k=44.900000 theta=119.8800 | k=32.617004 theta=121.6261 (7,9,11) ca-ca-ca k=63.670000 theta=120.0200 | k=91.230177 theta=120.7819 (10,9,11) ha-ca-ca k=44.900000 theta=119.8800 | k=32.071203 theta=117.5920 (2,11,9) ca-ca-ca k=63.670000 theta=120.0200 | k=103.822330 theta=118.0474 (2,11,12) ca-ca-oh k=78.860000 theta=119.9000 | k=77.987369 theta=124.2019 (9,11,12) ca-ca-oh k=78.860000 theta=119.9000 | k=86.514674 theta=117.7507 (11,12,13) ca-oh-ho k=67.410000 theta=108.5800 | k=69.116009 theta=109.4728 [Refinement] atomic charge fitting ... [Refinement] TorsionFit ... [Refinement] Using QM reference data for TorsionFit (mode=3) ... ============================================================================================================ 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=1.201055 n=2.000 phase=-179.0791 (2,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=0.335792 n=1.000 phase=16.5709 (2,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.020057 n=3.000 phase=-3.0284 (2,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.027304 n=4.000 phase=158.1465 (9,11,12,13) ca-ca-oh-ho term=1 k=0.855000 n=2.000 phase=180.0000 | k=1.191056 n=2.000 phase=-179.3972 (9,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=0.337479 n=1.000 phase=-163.9405 (9,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.022273 n=3.000 phase=173.7090 (9,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.028597 n=4.000 phase=168.1364 [Refinement] export GROMACS ... [Refinement] export Amber ... ====================================================================== PARMFIT REFINEMENT RESULT ====================================================================== Status: completed Input mol2: choi001_gaff2.mol2 Main products: Amber mol2: Refine4_work/Refine4_maple.mol2 Amber frcmod: Refine4_work/Refine4_maple.frcmod GROMACS top: Refine4_work/Refine4_maple.top GROMACS gro: Refine4_work/Refine4_maple.gro Amber tleap: Refine4_work/Refine4_maple_tleap.in Charge fitting: method: resp RESP level: HF/def2SVP target charge: 0 actual charge: 0.00000100 work MOL2: Refine4_work/chargefit/qm_route_charged.mol2 final MOL2: Refine4_work/Refine4_maple.mol2 Stage timing: TorsionFit 1h 34m 40s Hessian + mSeminario 1m 16s charge fitting 4s geometry optimization 2s export Amber 0s initial parameter assignment 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: Refine4_work/torsionfit/Refine4_mode3_qm_torsionfit_11-12_scan_final.xyz angle_deg QM_ref orig_ref stage0_ref stage1_ref stage2_ref 359.9822 0.000000 0.000000 0.000000 0.000000 0.000000 369.9822 0.195188 0.124719 0.138465 0.199665 0.206705 379.9822 0.745792 0.489457 0.548450 0.726819 0.746880 389.9822 1.564528 1.079790 1.202664 1.532104 1.567082 399.9822 2.547872 1.812961 2.020356 2.510284 2.557922 409.9822 3.592907 2.617694 2.921003 3.558628 3.613681 419.9822 4.611600 3.421253 3.810034 4.566192 4.622425 429.9822 5.495277 4.149309 4.610778 5.443823 5.496092 439.9822 6.160131 4.724004 5.259136 6.120211 6.165843 449.9822 6.565542 5.104617 5.694270 6.527226 6.565976 459.9822 6.676636 5.249737 5.902818 6.642428 6.675248 469.9822 6.496828 5.172303 5.902387 6.474951 6.502395 479.9822 6.057530 4.920910 5.744833 6.072990 6.094049 489.9822 5.441649 4.568802 5.484363 5.498948 5.511024 499.9822 4.817757 4.237583 5.105523 4.765308 4.765419 509.9822 4.056297 3.830521 4.872702 4.170751 4.156889 519.9822 3.519169 3.568440 4.571559 3.557099 3.530098 529.9822 3.157486 3.401974 4.381274 3.145276 3.108716 539.9822 2.949722 3.299391 4.401826 3.066559 3.026036 549.9822 3.078031 3.351873 4.467181 3.163996 3.125422 559.9822 3.445279 3.513180 4.657730 3.504769 3.472652 569.9822 3.991150 3.768721 4.949531 4.032874 4.009252 579.9822 4.638170 4.090024 5.308443 4.674310 4.658896 589.9822 5.300020 4.427443 5.682590 5.338518 5.329816 599.9822 5.888573 4.722025 6.004811 5.928433 5.925296 609.9822 6.320191 4.920328 6.201658 6.353049 6.355854 619.9822 6.532338 4.956917 6.223739 6.554734 6.565471 629.9822 6.479080 4.793433 6.027011 6.486881 6.508074 639.9822 6.137193 4.429499 5.595666 6.132191 6.165138 649.9822 5.494151 3.876465 4.927890 5.486021 5.529262 659.9822 4.624654 3.142883 4.078407 4.600833 4.649198 669.9822 3.653572 2.328507 3.183597 3.620876 3.667029 679.9822 2.631741 1.517393 2.277923 2.594853 2.631752 689.9822 1.657923 0.776946 1.445536 1.630970 1.654260 699.9822 0.859673 0.190781 0.786183 0.858569 0.868382 709.9822 0.336323 -0.185240 0.360393 0.365394 0.366462 719.9822 0.165506 -0.312330 0.215412 0.216380 0.216482 QM_ref vs stage2_final: MAE = 0.025352 kcal/mol, RMSE = 0.034396 kcal/mol TorsionFit: state: enabled torsion bonds: (11, 12) scan files: (11, 12): Refine4_work/torsionfit/Refine4_mode3_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 Refine4_maple_tleap.in parmed -p Refine4_maple_gas.prmtop <<< $'outparm Refine4_maple_gas_parmed.prmtop\nquit' ====================================================================== Program started: 2026-10-04 04:19:27 ====================================================================== TIMING SUMMARY ====================================================================== Input Reading....................................... 1.158 s ( 0.0 %) Settings Parsing.................................... 1.157 s ( 99.9 %) Coordinate Section Parsing.......................... 0.000 s ( 0.0 %) Post-Processing Expansion........................... 0.000 s ( 0.0 %) MLP Initialization.................................. 9.453 s ( 0.2 %) Job Dispatching..................................... 5762.894 s ( 99.8 %) Parmfit optimization................................ 5762.894 s ( 100.0 %) Parmfit correction.................................. 5762.855 s ( 100.0 %) ====================================================================== Total wall time: 5773.506 s Total CPU time: 20.370 s ====================================================================== Program ended: 2026-10-04 05:55:41 TOTAL RUN TIME: 0 days 1 hours 36 minutes 13 seconds 505 msec