$AFOMOD group              (relevant for FMO/AFO)                               
      This group allows user to define model systems for                        
some detached bonds, especially useful if the automatic                         
algorithm fails to build them. The group can have several                       
models given consequently. An example for one model is:                         
1 4                                                                             
   13   6.0     2.60639409    -1.41944144     0.87137460                        
    9   8.0     0.86256622    -1.53249713     0.69963114                        
   19   1.0     3.89530684    -3.08353483     0.30432753                        
    8   1.0     0.40393212     0.22566831    -0.24641973                        
Here, 1 is the bond in $FMOBND (numbered consequently) to                       
which the model is applied.  4 is the number of atoms in                        
the model.                                                                      
In the data set, the first number (above, 13 etc) is the                        
atomic number in $FMOXYZ, followed by atomic charge and                         
Cartesian coordinates.  New atoms such as hydrogen atoms                        
added as caps should be assigned formal numbers of some                         
heavy atoms present in the system, with the charge of 1.0                       
in $AFOMOD. These atoms will be identified as caps if the                       
charges in $FMOMOD and $FMOXYZ differ. For example, if you                      
add a new hydrogen cap and atom 12 in your system is                            
   12   1.0     0.40393212     0.22566831    -0.24641973                        
will define a hydrogen cap. Non-hydrogen caps can be done                       
likewise, just be sure that charges differ.                                     

generated on 7/7/2017