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$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:
$AFOMOD
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
$END
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
carbon,
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.
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generated on 7/7/2017