Example: Fragment Orbital analysis¶
Download Fragment_Orbitals.run
#!/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