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The Amber Force Fields

All Amber force field parameter files can be obtained by downloading AmberTools17, and extracting the .tar file. Parameter files will be in the amber16/dat/leap directory tree.

More information about Amber force fields can be found in Chapter 3 of the Amber 2017 Reference Manual, and in the following links:

  • The ff14SB force field is Amber's primary protein model, but there are in fact three protein force fields that are "seaworthy" when combined with standard water models. The ff15ipq force field was developed with a self-consistent physical model and rebuilds nearly all charge, angle, torsion, and some van-der Waals parameters for proteins. It is primarily tailored for SPC/Eb water. The ff15FB "Force Balance" force field is another re-derivation of the bonded parameters based on multiple sources of information.
  • Glycam parameters for carbohydrates (Also available is the Amber/Glycam Input Configurator, a web-based interface to help prepare inputs for simulations with the carbohydrate force fields. This feature is not updated with each new version of Amber. However, the settings and protocols it suggests are a way to get started.)
  • This paper describes the primary nucleic acids models in Amber. John SantaLucia and Berny Schlegel at Wayne State have also contributed modified RNA nucleosides.
  • This paper describes the primary lipids model in Amber, lipid14. For lipids not covered by this force field, the new lipid17 force field (unpublished as of yet) coveres a broader range of molecules and is available with the release.
  • Contributed parameters database, maintained by Richard Bryce at the University of Manchester
  • Forcefield_PTM: Amber-compatible parameters for post-translationally modified amino acids, prepared by the Floudas group at Princeton.
  • Zinc parameters, from Yuan-Ping Pang.
  • REDDB (Resp \ Esp charge Data Base), a database of resp charges and force field libraries for small molecules and biological molecular fragments, by P. Cieplak, F. Dupradeau and co-workers. (Hint: click on "List Projects"; "co-factor_biochemistry" has entries that are commonly requested by users.)
  • The ff99SBildn force field contains some modifications to ff99SB, described here: K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dror and D.E. Shaw. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78:1950, 2010. To use these, download the ff99SBildn.tar file, untar it in your $AMBERHOME directory, and type "source leaprc.ff99SBildn" in your LEaP input. (Please note: The ff14SB force field adds these sorts of corrections, and many others, to ff99SB, and is now the force field that Amber developers recommend for protein simulations.)
  • The ff99SBnmr force field contains another set of torsional modifications for ff99SB. See D.-W. Li and R. Bruschweiler. NMR-based protein potentials. Angew. Chem. Int. Ed. 49:6778, 2010.

Using the Amber force field in other software packages:

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Last modified: Aug 17, 2018