Step 9. Putting it all together: The whole ADF QM/MM input

The whole ADF QM/MM input for the sample system is given below. The following will be a QM/MM geometry optimization performed in Cartesian coordinates with no constraints. Some comments are provided in bold.

Title CYT amber95 test - CARTESIAN GEOMETRY OPTIMIZATION NO CONSTRAINTS
Fragments
 C T21.C.III.1s Notice that only fragments for the calculation of
 H T21.H.III model system are needed.
End

Symmetry NOSYM

Charge 0 0 This refers to the charge of the QM model system, not the 'real' 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 

QMMM
 FORCEFIELD_FILE 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
 DIIS N=5 OK=0.1 CYC=3
END

XC
 LDA VWN
 GGA POSTSCF Becke Perdew
End

Integration 3.0

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

In the above example, the geometry was defined with Cartesian coordinates and the geometry optimization was also done in Cartesians. The same input could also have easily been defined with a Z-matrix in the ATOMS key block.