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The Amber Force Fields

Amber is designed to work with several simple types of force fields, although it is most commonly used with parametrizations developed by Peter Kollman,his co-workers and “descendents”. The traditional parametrization uses fixed partial charges, centered on atoms. For a full description of the force fields and how to load them, please read Chapter 3 of the Amber Reference Manual.

Recommended Force Fields

Note: Be careful adopting a “mix and match” strategy for different components. The recommended choices are designed to work well together, and have been fairly extensively tested. Use of other combinations requires a deeper knowledge of the nature and origin of force fields. Recommended force fields are below:

Molecule/Ion Type
Force Field
protein ff19SB
carbohydrates GLYCAM_06j
lipids lipids21
organic molecules (usually ligands) gaff2
ions •should be matched to water model; see force fields for ions for further discussion
water model •should be matched to atomic ions; common water models include tip3p, spc/e, tip4pew, and OPC

More Force Field Information

  • Protein force fields
  • Nucleic acid force fields
  • Carbohydrate force fields
  • Lipid force fields
  • Ligand (usually organic molecules) force fields
  • Force fields for ions
  • Contributed Parameters
  • Accessing the Amber Force Fields

    All Amber force field parameter files can be obtained by downloading AmberTools22, and extracting the .tar file. Parameter files will be in the $AMBERHOME/dat/leap directory tree.

    • list of leaprc files available - $AMBERHOME/dat/leap/cmd
    • list of lib/off files available - $AMBERHOME/dat/leap/lib
    • list of frcmod/dat files available - $AMBERHOME/dat/leap/parm

    In order to add a parameter set into Leap, you will need both a lib file and a frcmod file. The leaprc files are premade scripts that call up the recommended combinations.

    In-Depth Description of Amber Force Field Files

    For an in-depth description of different force field file components, see Chapter 14 of the Amber Reference Manual.

    Using the Amber force fields in other software packages:

    "How's that for maxed out?"

    Last modified: May 12, 2022