Step 4. ADF QM/MM input: Atomic coordinates

Now we can begin to construct the input. We will begin with the atomic coordinates. For this example, we will optimize the geometry of the complex in Cartesian coordinates. Coordinates of the whole QM/MM complex or the 'real' complex should be defined here. DO NOT define the coordinates of the capping atoms. The program will calculate their positions, and add them automatically. The definition of the coordinates is done exactly as they are in a standard ADF run. Below is the ATOMS key block for our example system.

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