QMMM_CYT

Sample directory: adf/QMMM_CYT/

See the rest of the QM/MM manual , where this case is used as a ‘walk through’ for the QMMM feature.

It is a more or less straightforward application of QM/MM to geometry optimization (Cytocine). In the Atoms block all atoms are listed (QM as well as MM). All QM/MM aspects, such as which atoms belong to the QM core and which are to be treated by the approximate MM method, are found in the QMMM key block, and its various subkey blocks. The remainder of the input file is not different from what it would be in a non-QM/MM run.

The standard amber95 force field is used, which is located in the database of the ADF distribution.

$ADFBIN/adf << eor
Title  CYT amber95 - Cartesian Geometry Optimization

Fragments
  C   t21.C
  H   t21.H
End

Charge  0  0

Atoms Cartesian
   1 C       1.94807   3.58290  -0.58162
   2 C       1.94191   3.61595   1.09448
   3 H       1.69949   4.49893  -1.05273
   4 H       2.99455   3.17964  -0.86304
   5 C       0.94659   2.40054  -0.92364
   6 N      -1.74397  -3.46417   0.31178
   7 C      -1.00720  -2.20758   0.33536
   8 C      -1.66928  -1.00652   0.31001
   9 C      -0.92847   0.25653   0.34895
  10 N       0.43971   0.26735   0.38232
  11 N       0.36409  -2.20477   0.28992
  12 C       1.09714  -0.95413   0.22469
  13 H      -2.89781  -3.50815   0.31746
  14 H      -1.21484  -4.49217   0.31721
  15 H      -2.80940  -0.93497   0.30550
  16 H      -1.55324   1.21497   0.33885
  17 C       1.23309   1.44017   0.30994
  18 O       2.58277  -1.01636   0.23914
  19 H       2.37276   1.25557   0.29984
  20 O       1.02358   2.43085   1.50880
  21 H       1.17136   1.95097  -1.87367
  22 H      -0.10600   2.77333  -0.80348
  23 H       1.62170   4.54039   1.51392
  24 H       2.99608   3.28749   1.41345
End

QMMM
   FORCEFIELD_FILE  $ADFRESOURCES/ForceFields/amber95.ff
   RESTART_FILE mm.restart
   OUTPUT_LEVEL=1
   WARNING_LEVEL=2
   ELSTAT_COUPLING_MODEL=1

   LINK_BONDS
     1 - 5       1.38000      H
     1 - 2       1.38030      H
   SUBEND

   MM_CONNECTION_TABLE
     1    CT    QM     2   3   4   5
     2    CT    LI     1  20  23  24
     3    HC    QM     1
     4    HC    QM     1
     5    CT    LI     1  17  21  22
     6    N2    MM     7  13  14
     7    CA    MM     6   8  11
     8    CM    MM     7   9  15
     9    CM    MM     8  10  16
    10    N*    MM     9  12  17
    11    NC    MM     7  12
    12    C     MM    10  11  18
    13    H     MM     6
    14    H     MM     6
    15    HA    MM     8
    16    H4    MM     9
    17    CT    MM     5  10  19  20
    18    O     MM    12
    19    H2    MM    17
    20    OS    MM     2  17
    21    HC    MM     5
    22    HC    MM     5
    23    H1    MM     2
    24    H1    MM     2
 SUBEND

 CHARGES
   1  0.0  CT
   2  0.0  CT
   3  0.0  HC
   4  0.0  HC
   5  0.0  CT
   6 -0.9530  N2
   7  0.8185  CA
   8 -0.5215  CM
   9  0.0053  CM
  10 -0.0484  N*
  11 -0.7584  NC
  12  0.7538  C
  13  0.4234  H
  14  0.4234  H
  15  0.1928  HA
  16  0.1958  H4
  17  0.0066  CT
  18 -0.6252  O
  19  0.2902  H2
  20 -0.2033  OS
  21  0.0000  HC
  22  0.0000  HC
  23  0.0000  H1
  24  0.0000  H1
 SUBEND

END

Geometry
  Iterations   20
  Converge   E=1.0E-3  Grad=0.0005
  Step       Rad=0.3   Angle=5.0
End

XC
  LDA  VWN
  GGA  PostSCF Becke Perdew
End

BeckeGrid
  Quality Basic
End

SCF
  Iterations  60
  Converge  1.0E-06  1.0E-6
  Mixing  0.20
  DIIS  N=10  OK=0.500  CX=5.00  CXX=25.00  BFAC=0.00
End

End Input
eor