
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 153 surface points
Surface saved to: _potential_tmp.surf (153 points)
Computed Gauss-law surface charges from APBS potential and dielectric maps
Surface saved to: coupled_singlet.surf (153 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: 153
                Parallel Processing: True
============================================================


Logging results to: logs_20260905_163536
converged SCF energy = -1896.64637740281
Spin 0 (2S+1=1) converged: E = -1896.646377 Ha

Lowest energy: spin=0 (2S+1=1), E=-1896.646377 Ha
Saving GPU object type: <class 'gpu4pyscf.dft.rks.RKS'>
Saving functional (from parameter): b3lyp
Saved to molecule_alone.chk, Energy: -1896.6463774028111 (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: 0.135226
                s2_exe: 0.630146
                s3_exe: 0.773558
============================================================


Running combined calculation with all 153 surface points...
Summary log initialized: logs_20260905_163536/calculation_summary.out

=== Resurrecting /data/PHO_WORK/sajagbe2/QMMM/LOVCalculations/lf-proto/sog-protein/coupled-combined/MSOG/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/tmpufi07z3t.chk
max_memory 4000 MB (current use 1649 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= -1896.64637740259
  HOMO = 0.06734381787105  LUMO = 0.0781762901103284
cycle= 1 E= -1896.6463773881  delta_E= 1.45e-08  |g|= 0.000178  |ddm|= 0.000342
  HOMO = 0.0673929460382053  LUMO = 0.0781644050485116
cycle= 2 E= -1896.64636276599  delta_E= 1.46e-05  |g|= 0.00566  |ddm|= 0.0109
  HOMO = 0.0673452890120095  LUMO = 0.0781758379615006
cycle= 3 E= -1896.64637740223  delta_E= -1.46e-05  |g|= 3.95e-05  |ddm|= 0.0105
  HOMO = 0.0673453634962024  LUMO = 0.0781758362825148
cycle= 4 E= -1896.64637740258  delta_E= -3.44e-10  |g|= 9.57e-06  |ddm|= 4.31e-05
converged SCF energy = -1896.64637740258
Resurrected GPU DFT object: <class 'gpu4pyscf.dft.rks.RKS'>, Energy: -1896.6463774025783
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 1790 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 charge basis
Set gradient conv threshold to 3.16228e-05
init E= -1896.68135344752
  HOMO = 0.0526829236956005  LUMO = 0.0645178998826584
cycle= 1 E= -1896.67889493428  delta_E= 0.00246  |g|= 0.0758  |ddm|= 0.192
  HOMO = 0.0523128253047763  LUMO = 0.0883898852483891
cycle= 2 E= -1896.08500712724  delta_E= 0.594  |g|= 0.992  |ddm|= 2.02
  HOMO = 0.0544494284030631  LUMO = 0.0648970814601704
cycle= 3 E= -1896.67785535961  delta_E= -0.593  |g|= 0.0954  |ddm|= 2.02
  HOMO = 0.0545233890701633  LUMO = 0.0645406034268227
cycle= 4 E= -1896.68025807677  delta_E= -0.0024  |g|= 0.0526  |ddm|= 0.0748
  HOMO = 0.0532695163368731  LUMO = 0.0641439536281767
cycle= 5 E= -1896.68065664166  delta_E= -0.000399  |g|= 0.0486  |ddm|= 0.0486
  HOMO = 0.0537168167497679  LUMO = 0.0646657515033392
cycle= 6 E= -1896.68149816448  delta_E= -0.000842  |g|= 0.012  |ddm|= 0.0688
  HOMO = 0.0538885358227195  LUMO = 0.0648079635199912
cycle= 7 E= -1896.68154453824  delta_E= -4.64e-05  |g|= 0.0048  |ddm|= 0.0174
  HOMO = 0.0538578474149632  LUMO = 0.0647295686248367
cycle= 8 E= -1896.68155085117  delta_E= -6.31e-06  |g|= 0.00114  |ddm|= 0.00614
  HOMO = 0.0538906714824799  LUMO = 0.0647246982156862
cycle= 9 E= -1896.68155113619  delta_E= -2.85e-07  |g|= 0.000606  |ddm|= 0.00257
  HOMO = 0.053888952973263  LUMO = 0.0647066868389999
cycle= 10 E= -1896.68155116854  delta_E= -3.24e-08  |g|= 0.000477  |ddm|= 0.000636
  HOMO = 0.0538924786038245  LUMO = 0.0647120841936153
cycle= 11 E= -1896.68155124411  delta_E= -7.56e-08  |g|= 0.000234  |ddm|= 0.000456
  HOMO = 0.0538915246140717  LUMO = 0.0647117611878073
cycle= 12 E= -1896.68155125422  delta_E= -1.01e-08  |g|= 0.000178  |ddm|= 0.000119
  HOMO = 0.0538902863027753  LUMO = 0.0647129137048515
cycle= 13 E= -1896.68155126744  delta_E= -1.32e-08  |g|= 5.92e-05  |ddm|= 0.000387
  HOMO = 0.0538888274809199  LUMO = 0.0647115605873317
cycle= 14 E= -1896.68155126798  delta_E= -5.39e-10  |g|= 3.53e-05  |ddm|= 9.77e-05
  HOMO = 0.0538896343199176  LUMO = 0.0647121413244317
cycle= 15 E= -1896.68155126849  delta_E= -5.09e-10  |g|= 7.32e-06  |ddm|= 4.85e-05
converged SCF energy = -1896.68155126849
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 1802 MB)


Excited State energies (eV)
[0.13308937 0.63977481 0.75837043]
Combined effects: {'s1_exe_effect': -0.0020868986981338877, 's2_exe_effect': 0.00963580564390698, 's3_exe_effect': -0.015177417704669183}

Final statistics written to: logs_20260905_163536/calculation_summary.out
Raw properties appended to: logs_20260905_163536/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_16-39-11/
  Moved: ligand_tuning_summary.csv
  Moved 6 MOL2 files
  Added normalization parameters to summary
  Moved: logs_20260905_163536/ -> logs/
All expected output files were created.
