
4 GPU(s) detected.

Patched coupled.in -> num_procs = 4 (SLURM_GPUS_ON_NODE='4')
/home/users/sajagbe2/.local/lib/python3.11/site-packages/pyscf/dft/libxc.py:511: UserWarning: Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, corresponding to the original definition by Stephens et al. (issue 1480) and the same as the B3LYP functional in Gaussian. To restore the VWN5 definition, you can put the setting "B3LYP_WITH_VWN5 = True" in pyscf_conf.py
  warnings.warn('Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, '


============================================================
                   Electrostatic Map Suite
                    By Stephen O. Ajagbe
============================================================
============================================================
                  Electrostatic Tuning Maps
             Built on efforts by the Gozem Lab
   See: https://pubs.acs.org/doi/10.1021/acs.jpcb.9b00489
============================================================



4 GPU(s) detected.

Calculating Tuning of:  ['exe']
Using molecular states: {'neutral': True, 'td': True}


============================================================
                Calculation Type: combined
                Number of surface points: 150
                Parallel Processing: True
============================================================


Logging results to: logs_20260904_223152
converged SCF energy = -1896.6516896793
Spin 0 (2S+1=1) converged: E = -1896.651690 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.651690 Ha
Saving GPU object type: <class 'gpu4pyscf.dft.rks.RKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.6516896792996 (GPU)
Multi-GPU detected. Using subprocess for single-GPU TDDFT...
TDDFT completed in subprocess on GPU 0, states: 3


============================================================
                Raw Properties (No Surface)
                Total raw properties calculated: 3
                s1_exe: 0.134372
                s2_exe: 0.631740
                s3_exe: 0.774431
============================================================


Running combined calculation with all 150 surface points...
Summary log initialized: logs_20260904_223152/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/lov-protein/coupled-combined/AT1/singlet/molecule_alone.chk ===
Loaded XC functional: b3lyp
Creating DFT object with xc=b3lyp
Converting <class 'pyscf.dft.rks.RKS'> to GPU...
Successfully converted to GPU: <class 'gpu4pyscf.dft.rks.RKS'>


******** <class 'gpu4pyscf.dft.rks.RKS'> ********
method = RKS
initial guess = chkfile
damping factor = 0
level_shift factor = 0
DIIS = <class 'gpu4pyscf.scf.diis.CDIIS'>
diis_start_cycle = 1
diis_space = 8
diis_damp = 0
SCF conv_tol = 1e-09
SCF conv_tol_grad = None
SCF max_cycles = 50
direct_scf = True
direct_scf_tol = 1e-13
chkfile to save SCF result = /tmp/tmp_556v909.chk
max_memory 4000 MB (current use 1622 MB)
XC library gpu4pyscf.dft.libxc version 7.0.0 (CUDA)
    unable to decode the reference due to https://github.com/NVIDIA/cuda-python/issues/29
XC functionals = b3lyp
small_rho_cutoff = 1e-07
Set gradient conv threshold to 3.16228e-05
init E= -665.144436580689
  HOMO = -355.621348964158  LUMO = -273.55531171038
cycle= 1 E= 1386.17425073417  delta_E= 2.05e+03  |g|=   28  |ddm|= 6.89e+03
  HOMO = -13.2277899702826  LUMO = -13.1764305808926
cycle= 2 E= 401.988162357872  delta_E= -984  |g|= 36.4  |ddm|= 6.89e+03
  HOMO = -4.93722913644554  LUMO = -4.90673051522369
cycle= 3 E= -215.639817016385  delta_E= -618  |g|= 36.7  |ddm|=  264
  HOMO = -2.20192317574631  LUMO = -2.1804285311154
cycle= 4 E= -1029.4044407296  delta_E= -814  |g|= 34.7  |ddm|=  233
  HOMO = -0.876490080801483  LUMO = -0.867197550982694
cycle= 5 E= -1364.81827530155  delta_E= -335  |g|= 26.9  |ddm|=  120
  HOMO = -0.446645145577468  LUMO = -0.431833069935053
cycle= 6 E= -1296.43053525204  delta_E= 68.4  |g|= 27.7  |ddm|=  144
  HOMO = 0.0981649810619198  LUMO = 0.100752681480169
cycle= 7 E= -1770.04874888803  delta_E= -474  |g|=   14  |ddm|=  136
  HOMO = -0.256809484632988  LUMO = -0.246978385387986
cycle= 8 E= -1229.91116047856  delta_E=  540  |g|= 29.1  |ddm|=  237
  HOMO = 0.00768364326200323  LUMO = 0.00980854764004803
cycle= 9 E= -1764.30855614424  delta_E= -534  |g|=   15  |ddm|=  241
  HOMO = 0.178105138129957  LUMO = 0.189523169778476
cycle= 10 E= -968.171049447418  delta_E=  796  |g|= 32.9  |ddm|=  342
  HOMO = 0.294563954946348  LUMO = 0.297761639469176
cycle= 11 E= -1527.04347476895  delta_E= -559  |g|= 25.5  |ddm|=  159
  HOMO = 0.174104273552357  LUMO = 0.189972331335151
cycle= 12 E= -1664.9098220888  delta_E= -138  |g|=   16  |ddm|=  227
  HOMO = 0.105665559090001  LUMO = 0.110729075099716
cycle= 13 E= -1824.47999067926  delta_E= -160  |g|= 11.6  |ddm|= 78.9
  HOMO = 0.00589016417349581  LUMO = 0.0237367430530566
cycle= 14 E= -1771.86504082328  delta_E= 52.6  |g|= 14.8  |ddm|= 54.2
  HOMO = 0.127080223473882  LUMO = 0.130735139654052
cycle= 15 E= -1834.11434567562  delta_E= -62.2  |g|= 8.48  |ddm|= 49.1
  HOMO = 0.0643826589680754  LUMO = 0.0672478529443596
cycle= 16 E= -1524.94783726435  delta_E=  309  |g|= 22.8  |ddm|=   62
  HOMO = 0.0825490806731508  LUMO = 0.0914028697727204
cycle= 17 E= -1813.6801057687  delta_E= -289  |g|= 9.64  |ddm|= 44.6
  HOMO = 0.018259703474601  LUMO = 0.0279410204262238
cycle= 18 E= -1884.39279091295  delta_E= -70.7  |g|= 4.93  |ddm|= 31.5
  HOMO = 0.10203642344753  LUMO = 0.117256012745182
cycle= 19 E= -1868.09685648228  delta_E= 16.3  |g|= 6.67  |ddm|= 24.9
  HOMO = 0.100774239655297  LUMO = 0.131032366183535
cycle= 20 E= -1894.8153989876  delta_E= -26.7  |g|= 2.29  |ddm|=   16
  HOMO = 0.0397949320105836  LUMO = 0.0955066429328457
cycle= 21 E= -1896.03851328864  delta_E= -1.22  |g|= 1.47  |ddm|= 3.42
  HOMO = 0.00885432116340337  LUMO = 0.12561057516564
cycle= 22 E= -1896.43229630158  delta_E= -0.394  |g|= 0.826  |ddm|= 1.97
  HOMO = -0.00319717405844949  LUMO = 0.0991294347662943
cycle= 23 E= -1896.5221335916  delta_E= -0.0898  |g|= 0.563  |ddm|= 1.12
  HOMO = 0.0659836417847372  LUMO = 0.0947479005520544
cycle= 24 E= -1895.87673136696  delta_E= 0.645  |g|= 1.24  |ddm|= 2.47
  HOMO = 0.0349792005559386  LUMO = 0.0811741330695104
cycle= 25 E= -1896.58129868211  delta_E= -0.705  |g|= 0.382  |ddm|= 2.42
  HOMO = 0.0723255960288448  LUMO = 0.073417259417423
cycle= 26 E= -1896.60169346726  delta_E= -0.0204  |g|= 0.242  |ddm|= 0.311
  HOMO = 0.0665772216214702  LUMO = 0.102000766236338
cycle= 27 E= -1896.05738038801  delta_E= 0.544  |g|= 0.953  |ddm|= 2.37
  HOMO = 0.0711053024075082  LUMO = 0.0765587182888412
cycle= 28 E= -1896.10592955804  delta_E= -0.0485  |g|= 0.879  |ddm|= 0.237
  HOMO = 0.0714346425554521  LUMO = 0.0732704510743692
cycle= 29 E= -1896.63042120712  delta_E= -0.524  |g|= 0.189  |ddm|= 2.19
  HOMO = 0.0627557663328648  LUMO = 0.0758259765743301
cycle= 30 E= -1896.60393766306  delta_E= 0.0265  |g|= 0.27  |ddm|= 0.397
  HOMO = 0.0668798485049745  LUMO = 0.0743972850391993
cycle= 31 E= -1896.62051161635  delta_E= -0.0166  |g|= 0.224  |ddm|= 0.253
  HOMO = 0.0695160520898405  LUMO = 0.0752213699517763
cycle= 32 E= -1896.64048807499  delta_E= -0.02  |g|= 0.172  |ddm|= 0.868
  HOMO = 0.0696720823815797  LUMO = 0.082227706992211
cycle= 33 E= -1896.24048947473  delta_E=  0.4  |g|= 0.842  |ddm|= 1.39
  HOMO = 0.0670508843789584  LUMO = 0.0811514988401831
cycle= 34 E= -1896.22139892387  delta_E= 0.0191  |g|= 0.862  |ddm|= 0.091
  HOMO = 0.0685410945081925  LUMO = 0.0779156451646883
cycle= 35 E= -1896.44478035338  delta_E= -0.223  |g|= 0.675  |ddm|= 0.619
  HOMO = 0.0678904849762439  LUMO = 0.0761792688584775
cycle= 36 E= -1896.62352236652  delta_E= -0.179  |g|= 0.256  |ddm|= 0.699
  HOMO = 0.0682558236479946  LUMO = 0.0775427410349208
cycle= 37 E= -1896.58547824802  delta_E= 0.038  |g|= 0.397  |ddm|= 0.224
  HOMO = 0.067902669764824  LUMO = 0.0772620315525955
cycle= 38 E= -1896.64216370362  delta_E= -0.0567  |g|= 0.151  |ddm|= 0.399
  HOMO = 0.0675843173701374  LUMO = 0.0768289257909597
cycle= 39 E= -1896.64405653292  delta_E= -0.00189  |g|= 0.133  |ddm|= 0.055
  HOMO = 0.0649954831318711  LUMO = 0.0767346879483308
cycle= 40 E= -1896.65133069972  delta_E= -0.00727  |g|= 0.0323  |ddm|= 0.278
  HOMO = 0.0657743308903517  LUMO = 0.0772817516193908
cycle= 41 E= -1896.65096180486  delta_E= 0.000369  |g|= 0.0393  |ddm|= 0.0381
  HOMO = 0.0658143907711694  LUMO = 0.0768704855355041
cycle= 42 E= -1896.65143496823  delta_E= -0.000473  |g|= 0.0231  |ddm|= 0.0318
  HOMO = 0.0661287616205837  LUMO = 0.0768734190304696
cycle= 43 E= -1896.65168408014  delta_E= -0.000249  |g|= 0.00374  |ddm|= 0.0516
  HOMO = 0.0661506342251757  LUMO = 0.076898531818833
cycle= 44 E= -1896.6516793354  delta_E= 4.74e-06  |g|= 0.00477  |ddm|= 0.00355
  HOMO = 0.0661423984021273  LUMO = 0.0768918973938484
cycle= 45 E= -1896.65168607445  delta_E= -6.74e-06  |g|= 0.00281  |ddm|= 0.00377
  HOMO = 0.0661248095809388  LUMO = 0.0768945719899552
cycle= 46 E= -1896.65168951824  delta_E= -3.44e-06  |g|= 0.000584  |ddm|= 0.00416
  HOMO = 0.0661199386247813  LUMO = 0.0768936528626906
cycle= 47 E= -1896.65168965797  delta_E= -1.4e-07  |g|= 0.000216  |ddm|= 0.000729
  HOMO = 0.0661185861956578  LUMO = 0.07689363540758
cycle= 48 E= -1896.65168967589  delta_E= -1.79e-08  |g|= 9.18e-05  |ddm|= 0.000271
  HOMO = 0.0661167255549304  LUMO = 0.0768944018799144
cycle= 49 E= -1896.65168967304  delta_E= 2.84e-09  |g|= 0.000115  |ddm|= 0.000375
  HOMO = 0.0661176738357851  LUMO = 0.0768942220183581
cycle= 50 E= -1896.65168967925  delta_E= -6.21e-09  |g|= 1.8e-05  |ddm|= 0.000188

WARN: SCF failed to converge

SCF not converged.
SCF energy = -1896.65168967925
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.6516896792486
Multi-GPU detected. Using subprocess for single-GPU TDDFT...
TDDFT completed in subprocess on GPU 0, states: 3


******** <class 'gpu4pyscf.dft.rks.RKS'> ********
method = RKS
initial guess = chkfile
damping factor = 0
level_shift factor = 0
DIIS = <class 'gpu4pyscf.scf.diis.CDIIS'>
diis_start_cycle = 1
diis_space = 8
diis_damp = 0
SCF conv_tol = 1e-09
SCF conv_tol_grad = None
SCF max_cycles = 50
direct_scf = True
direct_scf_tol = 1e-13
chkfile to save SCF result = molecule_alone.chk
max_memory 4000 MB (current use 1731 MB)
XC library gpu4pyscf.dft.libxc version 7.0.0 (CUDA)
    unable to decode the reference due to https://github.com/NVIDIA/cuda-python/issues/29
XC functionals = b3lyp
small_rho_cutoff = 1e-07
Overwritten attributes  energy_nuc get_hcore  of <class 'gpu4pyscf.dft.rks.RKS'>
<class 'gpu4pyscf.dft.rks.RKS'> does not have attributes  spin basis charge
Set gradient conv threshold to 3.16228e-05
init E= -1896.69681204956
  HOMO = 0.0400488102423019  LUMO = 0.0656675325416436
cycle= 1 E= -1896.6621962519  delta_E= 0.0346  |g|= 0.253  |ddm|= 0.767
  HOMO = 0.0930071219790453  LUMO = 0.119510240177254
cycle= 2 E= -1888.44307732905  delta_E= 8.22  |g|= 3.23  |ddm|= 4.62
  HOMO = 0.0516645591192136  LUMO = 0.0609377322022906
cycle= 3 E= -1896.12187316353  delta_E= -7.68  |g|=    1  |ddm|= 4.03
  HOMO = 0.0521388572732645  LUMO = 0.062839611498416
cycle= 4 E= -1896.66612802695  delta_E= -0.544  |g|= 0.224  |ddm|= 2.19
  HOMO = 0.0560044513550183  LUMO = 0.0601387669158213
cycle= 5 E= -1896.57601369115  delta_E= 0.0901  |g|= 0.535  |ddm|= 1.45
  HOMO = 0.0549499713576844  LUMO = 0.059723134212716
cycle= 6 E= -1896.61574950368  delta_E= -0.0397  |g|= 0.441  |ddm|= 0.163
  HOMO = 0.0547633500277421  LUMO = 0.0603154150526281
cycle= 7 E= -1896.63403917133  delta_E= -0.0183  |g|= 0.394  |ddm|= 0.109
  HOMO = 0.0540653099338449  LUMO = 0.0621981758769533
cycle= 8 E= -1896.46373324989  delta_E= 0.17  |g|= 0.715  |ddm|= 0.583
  HOMO = 0.0540515248948921  LUMO = 0.0622469365288765
cycle= 9 E= -1896.45797459515  delta_E= 0.00576  |g|= 0.722  |ddm|= 0.0163
  HOMO = 0.0540220859819943  LUMO = 0.0622180843334728
cycle= 10 E= -1896.46694253924  delta_E= -0.00897  |g|= 0.71  |ddm|= 0.0251
  HOMO = 0.0532256621084609  LUMO = 0.0661457764320075
cycle= 11 E= -1896.21782195459  delta_E= 0.249  |g|= 0.904  |ddm|= 0.66
  HOMO = 0.0530322963519794  LUMO = 0.061011614385719
cycle= 12 E= -1896.63269387256  delta_E= -0.415  |g|= 0.389  |ddm|= 1.17
  HOMO = 0.045120833276668  LUMO = 0.0658586329257032
cycle= 13 E= -1896.67625967066  delta_E= -0.0436  |g|= 0.204  |ddm|= 1.09
  HOMO = 0.0483342247460678  LUMO = 0.0623894598988298
cycle= 14 E= -1896.68633635272  delta_E= -0.0101  |g|= 0.145  |ddm|= 0.148
  HOMO = 0.0491926421861772  LUMO = 0.062294977764962
cycle= 15 E= -1896.68896904742  delta_E= -0.00263  |g|= 0.127  |ddm|= 0.0499
  HOMO = 0.0515531167309511  LUMO = 0.0617238097298705
cycle= 16 E= -1896.69729431712  delta_E= -0.00833  |g|= 0.0268  |ddm|= 0.348
  HOMO = 0.0507024598291884  LUMO = 0.0618152872757556
cycle= 17 E= -1896.69705795426  delta_E= 0.000236  |g|= 0.0342  |ddm|= 0.122
  HOMO = 0.0512093729872461  LUMO = 0.061775822161816
cycle= 18 E= -1896.69748907224  delta_E= -0.000431  |g|= 0.0167  |ddm|= 0.103
  HOMO = 0.0512272353720147  LUMO = 0.061762680801309
cycle= 19 E= -1896.69741558895  delta_E= 7.35e-05  |g|= 0.0208  |ddm|= 0.00828
  HOMO = 0.0511477728307768  LUMO = 0.0617835533334405
cycle= 20 E= -1896.69754670588  delta_E= -0.000131  |g|= 0.0125  |ddm|= 0.0163
  HOMO = 0.0511955940292143  LUMO = 0.0617793217779611
cycle= 21 E= -1896.6975042348  delta_E= 4.25e-05  |g|= 0.0157  |ddm|= 0.00629
  HOMO = 0.0510152147103305  LUMO = 0.0618066610817244
cycle= 22 E= -1896.69762139964  delta_E= -0.000117  |g|= 0.000867  |ddm|= 0.0301
  HOMO = 0.0510230853413641  LUMO = 0.0618181808565631
cycle= 23 E= -1896.69762155949  delta_E= -1.6e-07  |g|= 0.000488  |ddm|= 0.00067
  HOMO = 0.0510116313467933  LUMO = 0.0618185713937351
cycle= 24 E= -1896.69762162493  delta_E= -6.54e-08  |g|= 0.000334  |ddm|= 0.0016
  HOMO = 0.0510162564158393  LUMO = 0.0618193772845683
cycle= 25 E= -1896.69762166797  delta_E= -4.3e-08  |g|= 0.000101  |ddm|= 0.000451
  HOMO = 0.0510166958314495  LUMO = 0.0618184032763187
cycle= 26 E= -1896.69762167295  delta_E= -4.98e-09  |g|= 1.94e-05  |ddm|= 0.000216
  HOMO = 0.0510166538036935  LUMO = 0.0618185154235346
cycle= 27 E= -1896.69762167297  delta_E= -1.82e-11  |g|= 1.76e-05  |ddm|= 3.11e-05
converged SCF energy = -1896.69762167297
Running TDDFT in current process (force_single_gpu=True)


******** <class 'gpu4pyscf.tdscf.rks.TDDFT'> for <class 'gpu4pyscf.dft.rks.RKS'> ********
nstates = 3 singlet
deg_eia_thresh = 1.000e-03
wfnsym = None
conv_tol = 1e-05
eigh lindep = 1e-12
eigh level_shift = 0
eigh max_cycle = 100
chkfile = molecule_alone.chk
max_memory 4000 MB (current use 1712 MB)


Excited State energies (eV)
[0.14583111 0.60262871 0.79453273]
Combined effects: {'s1_exe_effect': 0.011443607995777705, 's2_exe_effect': -0.0291125521540877, 's3_exe_effect': 0.020098673306862325}

Final statistics written to: logs_20260904_223152/calculation_summary.out
Raw properties appended to: logs_20260904_223152/calculation_summary.out
Created: ligand_s1_exe.mol2
Created: ligand_s2_exe.mol2
Created: ligand_s3_exe.mol2
Created: ligand_s1_exe_normalized.mol2
Created: ligand_s2_exe_normalized.mol2
Created: ligand_s3_exe_normalized.mol2

Created: ligand_tuning_summary.csv

Organizing results into: results_ligand_2026-09-04_22-36-05/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260904_223152/ -> logs/
All expected output files were created.
