Contents of the hoh.pdb2adf file generated by pdb2adf

The file is not given completely, since it contains more than 800 atoms.

#! /bin/sh

$ADFBIN/adf << eor
TITLE QM/MM calculation setup by pdb2adf: M.Swart, 2005

Symmetry NOSYM

EPRINT
  SFO NOEIG NOOVL
END

XC
 GGA Becke-Perdew
END

GEOMETRY
 CONVERGE grad=1.0e-3 rad=1.0e-1
END

BASIS
 type TZP
 core small
END

SCF
 Converge 1.0e-5 1.0e-5
 Iterations 99
END

INTEGRATION 5.0 5.0 5.0

CHARGE   0.0

ATOMS
     1 O      2.4390    25.7950    11.6340
     2 H      1.7160    26.2820    11.2390
     3 H      3.1400    26.4400    11.7290
     4 C    -10.0667    22.2493    11.7437
     5 H    -10.2077    21.5053    10.9597
     6 H    -10.5047    21.8683    12.6667
     7 H    -10.5167    23.2103    11.4977
     8 O     -8.7387    22.3983    12.0617
     9 H     -8.3007    22.6943    11.2607
    10 C     -0.2827    19.0253     2.2847
    11 H     -0.5357    18.2063     2.9567
    12 H      0.7633    19.2913     2.4407
    13 H     -0.9267    19.8753     2.5107
    14 O     -0.4997    18.6373     0.9467
    15 H      0.1123    17.9313     0.7287
....
   823 H      5.4711    27.9401    19.5645
   824 O      5.5611    28.7181    17.7095
   825 H      5.2631    27.8621    17.3935
END

QMMM
  FORCE_FIELD_FILE $ADFRESOURCES/ForceFields/amber95.ff
  RESTART_FILE mm.restart  ! old style restart
  OUTPUT_LEVEL=1
  WARNING_LEVEL=0
  ! -------------------
  ! for AddRemove model
  ! -------------------
  PARTITION=5
  ELSTAT_COUPLING_MODEL=4 ! for AddRemove model
 
  OPTIMIZE
    METHOD CONJGRAD
    MAX_STEPS 5000
    PRINT_CYCLES 10
    MM_NOTCONVERGED 0
  SUBEND

  MM_CONNECTION_TABLE
        1 OW  QM     2     3
        2 HW  QM     1
        3 HW  QM     1
        4 CT  MM     5     6     7     8
        5 H1  MM     4
        6 H1  MM     4
        7 H1  MM     4
        8 OH  MM     4     9
        9 HO  MM     8
       10 CT  MM    11    12    13    14
       11 H1  MM    10
       12 H1  MM    10
       13 H1  MM    10
       14 OH  MM    10    15
       15 HO  MM    14
....
      823 H1  MM   820
      824 OH  MM   820   825
      825 HO  MM   824
  SUBEND

  CHARGES
        1  -0.8340
        2   0.4170
        3   0.4170
        4   0.1166
        5   0.0372
        6   0.0372
        7   0.0372
        8  -0.6497
        9   0.4215
       10   0.1166
       11   0.0372
       12   0.0372
       13   0.0372
       14  -0.6497
       15   0.4215
...
      823   0.0372
      824  -0.6497
      825   0.4215
  SUBEND
END

COMMENT
  Atom  ADF ID  p2a ID  Amber     Mol   Nr   Amber    pdb ID    atom
    O        1       1     OW     HOH    1     SOL         2     O  
    H        2       2     HW     HOH    1     SOL         1     H1 
    H        3       3     HW     HOH    1     SOL         3     H2 
END

ENDINPUT
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