Input via the AMS system block

While usually options for an AMS engine are defined in its engine block, for the ForceField engine three ingredients are defined via the AMS system block: bonds, atom types and (partial) charges.

Here are some logical options

    1. Specify Everything: elements, coordinates, MM atom types, charges, and bonds

    1. Specify elements, coordinates, and bonds (UFF only)

    1. Specify elements and coordinates (UFF only, most convenient)

Currently, for most force fields, everything needs to be specified (option 1). UFF and GAFF allow the automatic determination of bonds and atom types (option 2 and 3). For GAFF this option is considered experimental as of the 2020 release and is disabled by default, see Antechamber integration below. See also the BondsUsage key on how bond information can be tweaked.

ForceField input example

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

$AMSBIN/ams << eor

Task GeometryOptimization

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

eor

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

2) Specify Elements, coordinates, and bonds (UFF only):

If we leave out the MM atom types and charges, UFF will determine the MM atom types automatically from the bond information:

$AMSBIN/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 ForceField
EndEngine

eor

3) Specify Elements and coordinates (UFF only):

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

$AMSBIN/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 ForceField
EndEngine

eor

The GUI generates inputs of the second or third type, depending on the “Use existing bonds” setting in the ForceField main tab. Note that to specify the MM Atom Types, the charges also need to be set. UFF has automatic bond guessing and a very simple automatic charge guessing only assigning charges to atoms of water molecules.

Antechamber integration

For the GAFF force field there is an experimental integration of the Antechamber toolkit for automatic atom typing. This allows the GAFF force field to be used with option 2 (only bonds and coordinates specified) and option 3 (coordinates only). As of the 2020 release of AMS, this option is still considered experimental and disabled by default. It can be enabled and configured from the input:

AntechamberIntegration Yes/No
AntechamberIntegration
Type

Bool

Default value

No

GUI name

Automatic atom typing

Description

EXPERIMENTAL: Use the Antechamber program to automatically determine atom types for the GAFF force field. This may run a geometry optimization with MOPAC under the hood in order to determine the charges (see keyword AntechamberTask), which might not work for very large systems.

AntechamberTask [GeometryOptimization | SinglePoint]
AntechamberTask
Type

Multiple Choice

Default value

GeometryOptimization

Options

[GeometryOptimization, SinglePoint]

Description

If antechamber is envoked to guess atomtypes and charges (GAFF force field), select the task for charge guessing with MOPAC