Input and Examples¶

The input style for the UFF program is similar to the input structure of the other parts in the ADF 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 ADF 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¶

The input should look something like this:

$ADFBIN/uff << eor

Units
    length Angstrom
End

System
  Atoms
    C   1.36012328  -0.14520095   0.60144543    C_3     0.000000
    C   0.00000000   0.00000000   0.00000000    C_2     0.000000
    H   2.09833847  -0.46327872  -0.16560721    H_      0.000000
    H   1.32657807  -0.90546800   1.40917410    H_      0.000000
    H   1.67935140   0.82750664   1.02977296    H_      0.000000
    H  -0.83486863   0.30434056   0.62258487    H_      0.000000
    O  -0.18030374  -0.22462371  -1.18585739    O_2     0.000000
  End

  Bonds
    1      2    1.000000000000
    1      3    1.000000000000
    1      5    1.000000000000
    1      4    1.000000000000
    2      7    2.000000000000
    2      6    1.000000000000
  End
End

Task
    RunType GO
END

Geometry
    Optim Cartesian
End

eor

The format in the Atoms section is: Element, x-coord, y-coord, z-coord, MM Atom Type, Charge. The format in the bonds section is: atom A, atom B, bond order. 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/uff << eor

Units
    length Angstrom
End

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

  Bonds
    1      2    1.000000000000
    1      3    1.000000000000
    1      5    1.000000000000
    1      4    1.000000000000
    2      7    2.000000000000
    2      6    1.000000000000
  End
End

Task
    RunType GO
END

Geometry
    Optim Cartesian
End

eor

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

$ADFBIN/uff << eor

Units
    length Angstrom
End

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

Task
    RunType GO
END

Geometry
    Optim Cartesian
End

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.