QMMM_CYTΒΆ
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