QMMM_CYT

Sample directory: adf/QMMM_CYT/

See the QMMM manual , where this case is used as a 'walk through' for the QMMM feature.

It is a more or less straightforward application of QMMM to geometry optimization (Cytocine). In the Atoms block all atoms are listed (QM as well as MM). All QMMM 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-QMMM 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

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
eor