********************************************************************** * * * 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 : Refine1.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: Refine1_work/Refine1_original.frcmod Topology atoms: 13 Topology bonds: 13 Bonded refinement: mSeminario QM reference: disabled 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] MLIP 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=234.900000 r=2.129000 | k=135.307826 r=2.089184 (2,3) ca-ca k=461.100000 r=1.398000 | k=387.211126 r=1.386447 (2,11) ca-ca k=461.100000 r=1.398000 | k=354.725565 r=1.392349 (3,4) ca-ha k=345.800000 r=1.086000 | k=387.425180 r=1.080401 (3,5) ca-ca k=461.100000 r=1.398000 | k=404.699707 r=1.383295 (5,6) ca-ha k=345.800000 r=1.086000 | k=387.865786 r=1.080000 (5,7) ca-ca k=461.100000 r=1.398000 | k=397.420428 r=1.387732 (7,8) ca-ha k=345.800000 r=1.086000 | k=385.826520 r=1.080601 (7,9) ca-ca k=461.100000 r=1.398000 | k=420.779909 r=1.381087 (9,10) ca-ha k=345.800000 r=1.086000 | k=387.397546 r=1.080825 (9,11) ca-ca k=461.100000 r=1.398000 | k=362.815889 r=1.393124 (11,12) ca-oh k=384.000000 r=1.364000 | k=359.072774 r=1.353310 (12,13) oh-ho k=371.400000 r=0.973000 | k=541.057803 r=0.967836 ------------------------------------------------------------------------------------------------------------ ANGLES ------------------------------------------------------------------------------------------------------------ (1,2,3) i-ca-ca k=57.500000 theta=119.1100 | k=43.159181 theta=119.2977 (1,2,11) i-ca-ca k=57.500000 theta=119.1100 | k=42.841349 theta=119.8516 (3,2,11) ca-ca-ca k=66.600000 theta=120.0200 | k=94.762258 theta=120.8507 (2,3,4) ca-ca-ha k=48.200000 theta=119.8800 | k=30.622040 theta=119.6543 (2,3,5) ca-ca-ca k=66.600000 theta=120.0200 | k=92.288304 theta=120.0635 (4,3,5) ha-ca-ca k=48.200000 theta=119.8800 | k=32.077476 theta=120.2823 (3,5,6) ca-ca-ha k=48.200000 theta=119.8800 | k=32.547326 theta=119.6914 (3,5,7) ca-ca-ca k=66.600000 theta=120.0200 | k=107.588870 theta=119.3629 (6,5,7) ha-ca-ca k=48.200000 theta=119.8800 | k=32.479813 theta=120.9457 (5,7,8) ca-ca-ha k=48.200000 theta=119.8800 | k=33.225618 theta=119.5956 (5,7,9) ca-ca-ca k=66.600000 theta=120.0200 | k=107.256271 theta=120.7410 (8,7,9) ha-ca-ca k=48.200000 theta=119.8800 | k=33.189603 theta=119.6633 (7,9,10) ca-ca-ha k=48.200000 theta=119.8800 | k=33.469243 theta=120.8004 (7,9,11) ca-ca-ca k=66.600000 theta=120.0200 | k=97.822480 theta=120.3046 (10,9,11) ha-ca-ca k=48.200000 theta=119.8800 | k=32.732252 theta=118.8951 (2,11,9) ca-ca-ca k=66.600000 theta=120.0200 | k=114.658407 theta=118.6773 (2,11,12) ca-ca-oh k=69.500000 theta=119.9000 | k=82.092199 theta=123.6636 (9,11,12) ca-ca-oh k=69.500000 theta=119.9000 | k=89.225194 theta=117.6591 (11,12,13) ca-oh-ho k=49.000000 theta=108.5800 | k=69.295820 theta=109.4221 [Refinement] TorsionFit ... ============================================================================================================ 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=0.900000 n=2.000 phase=180.0000 | k=0.831702 n=2.000 phase=179.9585 (2,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=1.020472 n=1.000 phase=2.1794 (2,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.062566 n=3.000 phase=-3.1822 (2,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.020202 n=4.000 phase=-168.6181 (9,11,12,13) ca-ca-oh-ho term=1 k=0.900000 n=2.000 phase=180.0000 | k=0.823596 n=2.000 phase=179.6884 (9,11,12,13) ca-ca-oh-ho term=2 k=NA n=NA phase=NA | k=1.021055 n=1.000 phase=-177.8841 (9,11,12,13) ca-ca-oh-ho term=3 k=NA n=NA phase=NA | k=0.063824 n=3.000 phase=177.9751 (9,11,12,13) ca-ca-oh-ho term=4 k=NA n=NA phase=NA | k=0.021260 n=4.000 phase=-170.0242 [Refinement] export GROMACS ... [Refinement] export Amber ... ====================================================================== PARMFIT REFINEMENT RESULT ====================================================================== Status: completed Input mol2: choi001_gaff2.mol2 Main products: Amber mol2: Refine1_work/Refine1_maple.mol2 Amber frcmod: Refine1_work/Refine1_maple.frcmod GROMACS top: Refine1_work/Refine1_maple.top GROMACS gro: Refine1_work/Refine1_maple.gro Amber tleap: Refine1_work/Refine1_maple_tleap.in Stage timing: Hessian + mSeminario 7s geometry optimization 2s TorsionFit 0s initial parameter assignment 0s export Amber 0s export GROMACS 0s charge fitting 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: Refine1_work/torsionfit/Refine1_torsionfit_11-12_scan_final.xyz angle_deg MLIP_ref orig_ref stage0_ref stage1_ref stage2_ref 359.9226 0.000000 0.000000 0.000000 0.000000 0.000000 369.9226 0.159524 0.185740 0.198823 0.154343 0.159719 379.9226 0.625432 0.748986 0.784806 0.595314 0.617047 389.9226 1.331669 1.618097 1.693869 1.273449 1.316369 399.9226 2.189532 2.710478 2.830700 2.114275 2.175081 409.9226 3.110161 3.920861 4.078425 3.024736 3.093157 419.9226 3.992471 5.133502 5.326029 3.919965 3.982378 429.9226 4.764528 6.234158 6.448918 4.698159 4.742319 439.9226 5.360273 7.159486 7.393041 5.322001 5.340871 449.9226 5.743585 7.855101 8.100211 5.740044 5.733192 459.9226 5.892447 8.307398 8.560909 5.939417 5.911643 469.9226 5.823906 8.505320 8.758393 5.892729 5.850801 479.9226 5.564513 8.497139 8.742562 5.637309 5.586431 489.9226 5.152944 8.342712 8.579648 5.231225 5.172879 499.9226 4.665431 8.115940 8.338024 4.745095 4.677190 509.9226 4.166853 7.877263 8.083878 4.258560 4.177577 519.9226 3.743183 7.677316 7.870970 3.848291 3.752272 529.9226 3.436608 7.552455 7.742001 3.582289 3.473042 539.9226 3.331109 7.509462 7.699650 3.483694 3.367189 549.9226 3.427432 7.556586 7.754694 3.571439 3.456122 559.9226 3.710890 7.688086 7.902955 3.834721 3.728687 569.9226 4.135550 7.887356 8.126624 4.236279 4.144673 579.9226 4.632563 8.122969 8.391693 4.716165 4.640078 589.9226 5.123345 8.346604 8.646642 5.198746 5.136117 599.9226 5.532484 8.496617 8.826515 5.604086 5.552092 609.9226 5.790450 8.506942 8.871243 5.870037 5.827692 619.9226 5.863582 8.315972 8.694679 5.919849 5.889377 629.9226 5.717592 7.885249 8.272023 5.744643 5.730811 639.9226 5.346481 7.198360 7.583904 5.339622 5.347196 649.9226 4.757455 6.252197 6.623667 4.704864 4.735416 659.9226 3.987726 5.116654 5.458195 3.901261 3.950852 669.9226 3.108171 3.890186 4.197371 3.019068 3.078220 679.9226 2.198307 2.665393 2.942680 2.132231 2.188634 689.9226 1.336134 1.533770 1.767216 1.283594 1.326340 699.9226 0.637028 0.633614 0.840487 0.613698 0.637457 709.9226 0.176900 0.048843 0.233285 0.171898 0.179092 719.9226 0.014581 -0.154275 0.017853 0.017929 0.017922 MLIP_ref vs stage2_final: MAE = 0.016114 kcal/mol, RMSE = 0.019326 kcal/mol TorsionFit: state: enabled torsion bonds: (11, 12) scan files: (11, 12): Refine1_work/torsionfit/Refine1_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 Refine1_maple_tleap.in parmed -p Refine1_maple_gas.prmtop <<< $'outparm Refine1_maple_gas_parmed.prmtop\nquit' ====================================================================== Program started: 2026-10-02 23:58:13 ====================================================================== TIMING SUMMARY ====================================================================== Input Reading....................................... 0.012 s ( 0.1 %) Settings Parsing.................................... 0.010 s ( 80.5 %) Coordinate Section Parsing.......................... 0.001 s ( 8.0 %) Post-Processing Expansion........................... 0.000 s ( 0.1 %) MLP Initialization.................................. 12.963 s ( 59.1 %) Job Dispatching..................................... 8.942 s ( 40.8 %) Parmfit optimization................................ 8.932 s ( 99.9 %) Parmfit correction.................................. 8.864 s ( 99.2 %) ====================================================================== Total wall time: 21.917 s Total CPU time: 24.638 s ====================================================================== Program ended: 2026-10-02 23:58:35 TOTAL RUN TIME: 0 days 0 hours 0 minutes 21 seconds 917 msec