#!/bin/sh

# An illustration of the fragment orbital analysis with DFTB

# The molecular system GC is build from 2 fragment: Guanine and Cytosine.
# An atomic Mulliken population is calculated for these two molecules.
# For these molecules the fragment orbitals are atomic.
# Next the full GC system is calculated and the fragment orbital analysis is
# calculated based on Guanine and Cytosine orbitals.

AMS_JOBNAME=Guanine  $AMSBIN/ams<<eor
System
  Atoms
     N      -2.58004483      -0.57534828       0.00000000
     O       1.37445517       1.80325172       0.00000000
     N      -0.64954483       0.71205172       0.00000000
     C      -2.02304483       0.65505172       0.00000000
     N      -2.79744483       1.73455172       0.00000000
     C      -2.08284483       2.87605172       0.00000000
     C      -0.68984483       3.05555172       0.00000000
     C       0.12945517       1.88485172       0.00000000
     N      -2.59534483       4.15055172       0.00000000
     C      -1.51504483       5.02095172       0.00000000
     N      -0.36064483       4.40135172       0.00000000
     H      -2.02304483      -1.44274828       0.00000000
     H      -3.58904483      -0.61664828       0.00000000
     H      -0.11144483      -0.18554828       0.00000000
     H      -3.58074483       4.38415172       0.00000000
     H      -1.65544483       6.09615172       0.00000000
  End
end

Task SinglePoint

Engine DFTB
   Model SCC-DFTB
   ResourcesDir DFTB.org/mio-1-1
   Properties
      Fragments
      End
   End
EndEngine
eor

AMS_JOBNAME=Cytosine $AMSBIN/ams<<eor
System
  Atoms
     O      -1.04004483      -2.99644828       0.00000000
     N       2.81855517      -0.50844828       0.00000000
     N       0.88085517      -1.73164828       0.00000000
     C       3.00115517      -2.92044828       0.00000000
     C       0.19685517      -2.90274828       0.00000000
     N       0.95725517      -4.09354828       0.00000000
     C       2.31775517      -4.09434828       0.00000000
     C       2.22455517      -1.70554828       0.00000000
     H       4.08765517      -2.90304828       0.00000000
     H       0.42435517      -4.95734827       0.00000000
     H       2.80565517      -5.06634827       0.00000000
     H       2.24745517       0.37825172       0.00000000
     H       3.82755517      -0.45254828       0.00000000
  End
end

Task SinglePoint

Engine DFTB
   Model SCC-DFTB
   ResourcesDir DFTB.org/mio-1-1
   Properties
      Fragments
      End
   End
EndEngine
eor

AMS_JOBNAME=GC $AMSBIN/ams<<eor
System
  Atoms
     N      -2.58004483      -0.57534828       0.00000000
     O       1.37445517       1.80325172       0.00000000
     N      -0.64954483       0.71205172       0.00000000
     C      -2.02304483       0.65505172       0.00000000
     N      -2.79744483       1.73455172       0.00000000
     C      -2.08284483       2.87605172       0.00000000
     C      -0.68984483       3.05555172       0.00000000
     C       0.12945517       1.88485172       0.00000000
     N      -2.59534483       4.15055172       0.00000000
     C      -1.51504483       5.02095172       0.00000000
     N      -0.36064483       4.40135172       0.00000000
     H      -2.02304483      -1.44274828       0.00000000
     H      -3.58904483      -0.61664828       0.00000000
     H      -0.11144483      -0.18554828       0.00000000
     H      -3.58074483       4.38415172       0.00000000
     H      -1.65544483       6.09615172       0.00000000
     O      -1.04004483      -2.99644828       0.00000000
     N       2.81855517      -0.50844828       0.00000000
     N       0.88085517      -1.73164828       0.00000000
     C       3.00115517      -2.92044828       0.00000000
     C       0.19685517      -2.90274828       0.00000000
     N       0.95725517      -4.09354828       0.00000000
     C       2.31775517      -4.09434828       0.00000000
     C       2.22455517      -1.70554828       0.00000000
     H       4.08765517      -2.90304828       0.00000000
     H       0.42435517      -4.95734827       0.00000000
     H       2.80565517      -5.06634827       0.00000000
     H       2.24745517       0.37825172       0.00000000
     H       3.82755517      -0.45254828       0.00000000
  End
end

Task SinglePoint

Engine DFTB
   Model SCC-DFTB
   ResourcesDir DFTB.org/mio-1-1
   Properties
      Fragments
         File Guanine.results/dftb.rkf
         File Cytosine.results/dftb.rkf
      End
   End
EndEngine
eor