cp2k_qmmm_setup.py v1.0  (2026-10-25 11:18)
Topology    : AMBER.prmtop  (42455 atoms, 12932 residues)
Coordinates : AMBER.rst7
MM cell     : 77.6793 82.5830 81.2552  angles 90.00 90.00 90.00
QM selection: Amber mask: :LIG | (:44,100,206 & !@N,H,CA,HA,C,O)
QM atoms    : 74

QM residues (QM atoms / residue atoms):
       HID44   11/17   CB HB2 HB3 CG ND1 HD1 CE1 HE1 NE2 CD2 HD2
      ASP100    6/12   CB HB2 HB3 CG OD1 OD2
      SER206    5/11   CB HB2 HB3 OG HG
      LIG291   52/52   (whole residue)

QM/MM links (cut bonds): 3
  QM    3274 SER206@CB   (2C )  MM    3272 SER206@CA   (CX )  r0(QM-MM)=1.526  r0(QM-H)=1.090 [2C-H (topology)]  ALPHA_IMOMM=1.400
  QM    1645 ASP100@CB   (2C )  MM    1643 ASP100@CA   (CX )  r0(QM-MM)=1.526  r0(QM-H)=1.090 [2C-H (topology)]  ALPHA_IMOMM=1.400
  QM     654 HID44@CB   (CT )  MM     652 HID44@CA   (CX )  r0(QM-MM)=1.526  r0(QM-H)=1.090 [CT-H (topology)]  ALPHA_IMOMM=1.400

Charge bookkeeping (e):
  total charge of the system           : -0.000000
  sum of MM charges of the QM atoms    : +0.204400
  boundary residues (MM part -> target):
         HID44  residue -0.0000  MM part -0.0075 -> +0  (correction +0.0075 on 6 atom(s))
        ASP100  residue -1.0000  MM part -0.1419 -> +0  (correction +0.1419 on 6 atom(s))
        SER206  residue -0.0000  MM part -0.0550 -> +0  (correction +0.0550 on 6 atom(s))
  MM region charge after correction    : -0.000000
  nominal QM charge (total - MM)       : -0.000000  ->  &DFT CHARGE 0

QM cell:
  extent of QM atoms + caps            : 12.371 12.570 10.562
  QM cell (padding 5.0 A per side)    : 22.500 23.000 21.000
  suggested QM Ewald GMAX (DFTB/SE)    : 22 23 21
  suggested MM Ewald GMAX              : 78 83 81

Corrected topology written: AMBER_ee.prmtop
  MM region charge +0.000002; the QM atoms keep their original MM charges (+0.204400), which CP2K does not use with electrostatic embedding

Files written:
  forceeval_qmmm.cp2k.inc          &CELL, &QM_KIND and &LINK sections (include inside &QMMM)
  kinds.cp2k.inc                   &KIND sections for the 246 CP2K kinds of AMBER.prmtop (include inside &SUBSYS)
  kinds_ee.cp2k.inc                &KIND sections for the 262 CP2K kinds of AMBER_ee.prmtop
  qm_region.xyz                    QM region with capping H (visual check, standalone QM tests)
  charge_correction.parmed         ParmEd commands for the charge correction (18 atoms)
  AMBER_ee.prmtop                  charge-corrected topology for ECOUPL COULOMB/GAUSS
  qmmm_setup_summary.txt           this summary

No warnings.

Set in &FORCE_EVAL/&DFT:  CHARGE 0   (and the MULTIPLICITY of your QM region)
