Amber masthead
Filler image AmberTools21 Amber20 Manuals Tutorials Force Fields Contacts History
Filler image

Useful links:

Amber Home
Download Amber
Installation
Amber Citations
GPU Support
Updates
Mailing Lists
For Educators
File Formats
 

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 2021 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
DNA OL15
RNA OL3
carbohydrates GLYCAM_06j
lipids lipids17
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
  • Contributed Parameters
  • Accessing the Amber Force Fields

    All Amber force field parameter files can be obtained by downloading AmberTools21, 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 15 of the Amber 2021 Reference Manual.

    Using the Amber force fields in other software packages:

    "How's that for maxed out?"

    Last modified: Aug 27, 2021