Input and examples

The input style for the UFF program is similar to the input structure of the other parts in the AMS package. Some helpful examples of UFF calculations can be found in the $ADFHOME/examples/uff directory. The input can also be studied by setting up a job with the UFF tab in the GUI, followed by clicking on “Details” - “Run Script”. The UFF input can have multiple forms in the AMS package. Depending on what information is given, UFF fills in the rest. The main options are:

  • Specify Elements, coordinates, MM Atom Types, Charges, and bonds
  • Specify Elements, coordinates, and bonds
  • Specify Elements and coordinates

UFF input example

Specify Elements, coordinates, MM Atom Types, Charges, and bonds:

$ADFBIN/ams << eor

Task GeometryOptimization

System
    Atoms
        C   1.36012328  -0.14520095   0.60144543    Type=C_3     Charge=0.000000
        C   0.00000000   0.00000000   0.00000000    Type=C_2     Charge=0.000000
        H   2.09833847  -0.46327872  -0.16560721    Type=H_      Charge=0.000000
        H   1.32657807  -0.90546800   1.40917410    Type=H_      Charge=0.000000
        H   1.67935140   0.82750664   1.02977296    Type=H_      Charge=0.000000
        H  -0.83486863   0.30434056   0.62258487    Type=H_      Charge=0.000000
        O  -0.18030374  -0.22462371  -1.18585739    Type=O_2     Charge=0.000000
    End
    BondOrders
         1 5 1.0
         1 4 1.0
         1 3 1.0
         1 2 1.0
         2 6 1.0
         2 7 2.0
    End
End

Engine UFF
EndEngine

eor

The format in the bonds section is: atom A, atom B, bond order.

Specify Elements, coordinates, and bonds:

If we leave out the MM atom types and charges, UFF will determine the MM atom types automatically from the bond information. Except for leaving out MM atom types and charges, the second input format is similar to the first input format:

$ADFBIN/ams << eor

Task GeometryOptimization

System
    Atoms
        C  1.36012328 -0.14520095  0.60144543
        C  0.00000000  0.00000000  0.00000000
        H  2.09833847 -0.46327872 -0.16560721
        H  1.32657807 -0.90546800  1.40917410
        H  1.67935140  0.82750664  1.02977296
        H -0.83486863  0.30434056  0.62258487
        O -0.18030374 -0.22462371 -1.18585739
    End
    BondOrders
         1 5 1.0
         1 4 1.0
         1 3 1.0
         1 2 1.0
         2 6 1.0
         2 7 2.0
    End
End

Engine UFF
EndEngine

eor

Specify Elements and coordinates:

The third input format is similar to the second, but without a Bonds section in System:

$ADFBIN/ams << eor

Task GeometryOptimization

System
    Atoms
        C  1.36012328 -0.14520095  0.60144543
        C  0.00000000  0.00000000  0.00000000
        H  2.09833847 -0.46327872 -0.16560721
        H  1.32657807 -0.90546800  1.40917410
        H  1.67935140  0.82750664  1.02977296
        H -0.83486863  0.30434056  0.62258487
        O -0.18030374 -0.22462371 -1.18585739
    End
End

Engine UFF
EndEngine

eor

The GUI generates inputs of the second or third type, depending on the “Use existing bonds” setting in the UFF main tab. Note that to specify the MM Atom Types, the charges also need to be set. UFF will not assign charges to atoms on its own, so fixing the charges to 0.000 will not change behavior.