
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 Potential Module
============================================================

Generating VDW surface for potential mapping...
Generating VDW surface (density=0.5, scale=1.0)...
Generated 147 surface points
Surface saved to: _potential_tmp.surf (147 points)
Computed Gauss-law surface charges from APBS potential and dielectric maps
Surface saved to: coupled_singlet.surf (147 points)
Potential map CSV: coupled_singlet.csv
============================================================
============================================================
                  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: 147
                Parallel Processing: True
============================================================


Logging results to: logs_20260905_163538
converged SCF energy = -1896.64188333712
Spin 0 (2S+1=1) converged: E = -1896.641883 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.641883 Ha
Saving GPU object type: <class 'gpu4pyscf.dft.rks.RKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.6418833371167 (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: 0.136674
                s2_exe: 0.580039
                s3_exe: 0.819700
============================================================


Running combined calculation with all 147 surface points...
Summary log initialized: logs_20260905_163538/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/sog-protein/coupled-combined/SOPP3/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_j9n7z_s.chk
max_memory 4000 MB (current use 1711 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= 939563.554165851
  HOMO = -17.5875431771925  LUMO = -16.8292433322753
cycle= 1 E= 854.315009840293  delta_E= -9.39e+05  |g|= 50.6  |ddm|= 5.09e+03
  HOMO = -10.4902086062296  LUMO = -10.3696556845515
cycle= 2 E= 1292.09149390707  delta_E=  438  |g|= 29.2  |ddm|= 5.1e+03
  HOMO = -7.14037373782203  LUMO = -7.11744285727988
cycle= 3 E= 319.163328608317  delta_E= -973  |g|=   36  |ddm|=  298
  HOMO = -1.29470334533799  LUMO = -1.28782522942944
cycle= 4 E= -922.777504202012  delta_E= -1.24e+03  |g|= 32.8  |ddm|=  226
  HOMO = 0.133143729263613  LUMO = 0.151860275152636
cycle= 5 E= -917.67399872493  delta_E=  5.1  |g|= 30.6  |ddm|=  491
  HOMO = -0.107769207324074  LUMO = -0.095885453797051
cycle= 6 E= -1604.3453042508  delta_E= -687  |g|= 19.9  |ddm|=  480
  HOMO = -0.0974639317547427  LUMO = -0.0924041582317274
cycle= 7 E= -1118.75147803549  delta_E=  486  |g|= 32.4  |ddm|=  168
  HOMO = 0.140944216679446  LUMO = 0.143434027121549
cycle= 8 E= -1788.96976015194  delta_E= -670  |g|= 13.8  |ddm|=  146
  HOMO = 0.232741254423291  LUMO = 0.241015967894618
cycle= 9 E= -1814.38559235299  delta_E= -25.4  |g|= 10.8  |ddm|= 60.1
  HOMO = -0.0976643966377235  LUMO = -0.0805150306877055
cycle= 10 E= -1102.81663230756  delta_E=  712  |g|= 33.2  |ddm|=  302
  HOMO = -0.0274108283460298  LUMO = -0.0231188465339994
cycle= 11 E= -1596.49274718416  delta_E= -494  |g|= 22.2  |ddm|=  303
  HOMO = 0.0849405837462841  LUMO = 0.0893942532268381
cycle= 12 E= -1858.53332934056  delta_E= -262  |g|= 7.04  |ddm|= 56.2
  HOMO = 0.0838433155024627  LUMO = 0.0947980204735389
cycle= 13 E= -1718.07132058927  delta_E=  140  |g|= 14.6  |ddm|= 73.8
  HOMO = 0.0403881422099629  LUMO = 0.0437688460115115
cycle= 14 E= -1871.44976694722  delta_E= -153  |g|= 7.13  |ddm|= 66.3
  HOMO = 0.115500221290601  LUMO = 0.121257739688818
cycle= 15 E= -1876.9045478109  delta_E= -5.45  |g|= 5.08  |ddm|= 22.8
  HOMO = 0.14897564902859  LUMO = 0.159679250570792
cycle= 16 E= -1889.35340982484  delta_E= -12.4  |g|= 4.07  |ddm|= 17.7
  HOMO = 0.118373099333348  LUMO = 0.14160150002052
cycle= 17 E= -1895.37135352156  delta_E= -6.02  |g|= 2.14  |ddm|= 16.9
  HOMO = 0.0720311226994653  LUMO = 0.133377002412589
cycle= 18 E= -1896.35240488311  delta_E= -0.981  |g|= 0.938  |ddm|= 3.29
  HOMO = 0.0562138539422502  LUMO = 0.106810283226399
cycle= 19 E= -1896.4930892824  delta_E= -0.141  |g|= 0.693  |ddm|= 1.44
  HOMO = 0.074903072124946  LUMO = 0.0770595423069104
cycle= 20 E= -1896.57481938911  delta_E= -0.0817  |g|= 0.335  |ddm|= 0.788
  HOMO = 0.0783434246287009  LUMO = 0.103847484671566
cycle= 21 E= -1896.01257466235  delta_E= 0.562  |g|= 1.03  |ddm|= 2.38
  HOMO = 0.0718888673905798  LUMO = 0.0792683637124137
cycle= 22 E= -1896.57929234609  delta_E= -0.567  |g|= 0.321  |ddm|= 2.37
  HOMO = 0.0678777976021841  LUMO = 0.0894084436101129
cycle= 23 E= -1896.07894250302  delta_E=  0.5  |g|= 0.91  |ddm|= 2.37
  HOMO = 0.0711724636967997  LUMO = 0.0833081957434172
cycle= 24 E= -1896.08446790594  delta_E= -0.00553  |g|= 0.896  |ddm|= 0.145

WARN: HOMO 0.0734595205266786 == LUMO 0.0743352776955086

cycle= 25 E= -1896.6411891319  delta_E= -0.557  |g|= 0.0467  |ddm|= 2.04
  HOMO = 0.0709102083981907  LUMO = 0.0781331403337337
cycle= 26 E= -1896.61047685684  delta_E= 0.0307  |g|= 0.271  |ddm|= 0.505
  HOMO = 0.0712524198540509  LUMO = 0.0789561083493497
cycle= 27 E= -1896.48097445334  delta_E= 0.13  |g|= 0.601  |ddm|= 0.544
  HOMO = 0.0699029385975499  LUMO = 0.0780353052969533
cycle= 28 E= -1896.61687351437  delta_E= -0.136  |g|= 0.242  |ddm|= 0.593
  HOMO = 0.0664131146378036  LUMO = 0.0783769609541121
cycle= 29 E= -1896.63683523101  delta_E= -0.02  |g|= 0.101  |ddm|= 0.608
  HOMO = 0.068859471467257  LUMO = 0.0784482458085587
cycle= 30 E= -1896.63635079493  delta_E= 0.000484  |g|= 0.111  |ddm|= 0.406
  HOMO = 0.0685440173916854  LUMO = 0.078779095587732
cycle= 31 E= -1896.63928697469  delta_E= -0.00294  |g|= 0.0754  |ddm|= 0.063
  HOMO = 0.0680267917279932  LUMO = 0.0785592373997188
cycle= 32 E= -1896.64164139063  delta_E= -0.00235  |g|= 0.0229  |ddm|= 0.0967
  HOMO = 0.0679409903807732  LUMO = 0.0785951908547572
cycle= 33 E= -1896.641810288  delta_E= -0.000169  |g|= 0.0125  |ddm|= 0.0191
  HOMO = 0.0676843009016226  LUMO = 0.0786323502402101
cycle= 34 E= -1896.64179976194  delta_E= 1.05e-05  |g|= 0.0135  |ddm|= 0.0488
  HOMO = 0.0677901571150872  LUMO = 0.0785942592978579
cycle= 35 E= -1896.64188313813  delta_E= -8.34e-05  |g|= 0.000689  |ddm|= 0.0242
  HOMO = 0.0678040855964538  LUMO = 0.0786025907180142
cycle= 36 E= -1896.64188330748  delta_E= -1.69e-07  |g|= 0.000244  |ddm|= 0.000886
  HOMO = 0.0678102103246134  LUMO = 0.078600948558722
cycle= 37 E= -1896.64188326385  delta_E= 4.36e-08  |g|= 0.000396  |ddm|= 0.00123
  HOMO = 0.0678064661133187  LUMO = 0.0786016151252749
cycle= 38 E= -1896.64188333613  delta_E= -7.23e-08  |g|= 5.12e-05  |ddm|= 0.000689
  HOMO = 0.0678067136273554  LUMO = 0.0786020840667528
cycle= 39 E= -1896.6418833366  delta_E= -4.67e-10  |g|= 3.03e-05  |ddm|= 0.000123
converged SCF energy = -1896.6418833366
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.6418833365965
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 1812 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  basis charge spin
Set gradient conv threshold to 3.16228e-05
init E= -1896.66251808751
  HOMO = 0.0577509630385589  LUMO = 0.0723360125560728
cycle= 1 E= -1896.64713173844  delta_E= 0.0154  |g|= 0.171  |ddm|= 0.417
  HOMO = 0.0999581687153239  LUMO = 0.10861449284589
cycle= 2 E= -1893.165981749  delta_E= 3.48  |g|= 2.19  |ddm|= 3.52
  HOMO = 0.0620781288722265  LUMO = 0.0700857501345746
cycle= 3 E= -1896.35776914164  delta_E= -3.19  |g|= 0.809  |ddm|= 2.94
  HOMO = 0.0623805013090106  LUMO = 0.0709540085186044
cycle= 4 E= -1896.66212910935  delta_E= -0.304  |g|= 0.0387  |ddm|= 1.37
  HOMO = 0.0623352530428809  LUMO = 0.0709024982283763
cycle= 5 E= -1896.6426198528  delta_E= 0.0195  |g|= 0.216  |ddm|= 0.427
  HOMO = 0.0620732703403714  LUMO = 0.0707852793637494
cycle= 6 E= -1896.64488631792  delta_E= -0.00227  |g|= 0.204  |ddm|= 0.0257
  HOMO = 0.0617853634824061  LUMO = 0.0709314600018593
cycle= 7 E= -1896.65279973917  delta_E= -0.00791  |g|= 0.152  |ddm|= 0.0881
  HOMO = 0.0614582820577484  LUMO = 0.0711326151952104
cycle= 8 E= -1896.65671588721  delta_E= -0.00392  |g|= 0.116  |ddm|= 0.0612
  HOMO = 0.0611670501621428  LUMO = 0.071262207187091
cycle= 9 E= -1896.66043706565  delta_E= -0.00372  |g|= 0.0703  |ddm|= 0.0787
  HOMO = 0.0604726904003563  LUMO = 0.0714960636566011
cycle= 10 E= -1896.66266584963  delta_E= -0.00223  |g|= 0.00606  |ddm|= 0.137
  HOMO = 0.0602362215156836  LUMO = 0.0714160033201277
cycle= 11 E= -1896.66221794835  delta_E= 0.000448  |g|= 0.0312  |ddm|= 0.0528
  HOMO = 0.060572192765859  LUMO = 0.0713533830232514
cycle= 12 E= -1896.66267850134  delta_E= -0.000461  |g|= 0.000516  |ddm|= 0.0612
  HOMO = 0.0605679458905472  LUMO = 0.0713686554596849
cycle= 13 E= -1896.66267709662  delta_E= 1.4e-06  |g|= 0.00177  |ddm|= 0.00401
  HOMO = 0.0605959356998849  LUMO = 0.0713583721657972
cycle= 14 E= -1896.6626779591  delta_E= -8.62e-07  |g|= 0.00116  |ddm|= 0.00562
  HOMO = 0.0605875866708337  LUMO = 0.071358998328354
cycle= 15 E= -1896.66267851048  delta_E= -5.51e-07  |g|= 0.000402  |ddm|= 0.00145
  HOMO = 0.0605844124052872  LUMO = 0.071359841977233
cycle= 16 E= -1896.66267858228  delta_E= -7.18e-08  |g|= 8.09e-05  |ddm|= 0.000608
  HOMO = 0.0605839882975376  LUMO = 0.0713601360623337
cycle= 17 E= -1896.66267858509  delta_E= -2.8e-09  |g|= 3.05e-05  |ddm|= 0.000129
  HOMO = 0.0605839730908353  LUMO = 0.0713600072342924
cycle= 18 E= -1896.66267858508  delta_E= 9.09e-12  |g|= 2.64e-05  |ddm|= 3.28e-05
converged SCF energy = -1896.66267858508
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 1823 MB)


Excited State energies (eV)
[0.13591258 0.56561943 0.8335402 ]
Combined effects: {'s1_exe_effect': -0.0007299448257700458, 's2_exe_effect': -0.014414935191352729, 's3_exe_effect': 0.0138507216111744}

Final statistics written to: logs_20260905_163538/calculation_summary.out
Raw properties appended to: logs_20260905_163538/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_2026-09-05_16-39-18/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260905_163538/ -> logs/
All expected output files were created.
