The Amber Force Fields
All Amber force field parameter files can be obtained by
downloading AmberTools20, and extracting
.tar file. Parameter files will be in the
amber20_src/dat/leap directory tree.
More information about Amber
force fields can be found in Chapter 3 of the Amber 2020 Reference
Manual, and in the following links:
field are Amber's primary protein model. The new ff19SB forcefield
has shown to improve amino-acid dependent properties such as helical propensities
and reproduces the differences in amino acid-specific Ramachandram Map using amino
acid specific CMAPS. ff19SB pairs best with the more accurate OPC water model.
The ff14SB model is intended for use with TIP3P water;
ff14SBonlysc is the same
model but without the empirical backbone corrections for TIP3P; this is a good choice
when ff14SB is desired but using other water models such as TIP4PEW. There
are also three other protein force fields that are "seaworthy" when combined with
standard water models. The
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
"Force Balance" force field is another re-derivation of the bonded parameters
based on multiple sources of information.
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
nucleic acids models in Amber. John SantaLucia and Berny Schlegel at
Wayne State have also contributed
- This paper describes the
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field, the new lipid17 force field (unpublished as of yet) coveres a broader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.
parameters database, maintained by Richard Bryce at the University of
New forcefield parameters for phosphorylated Histidine, Serine, Threonine, and Tyrosine
that show improvements over the Homeyer parameters. New parameters for modified amino
acids selenomethionine, cyano-phenylalanine, azido-phenylalanine, acetylated lysine,
and methanesulfonothioate spin label. Selenium LJ parametes are now available in Amber.
These parameters are located in the amber20_src/dat/leap directory. Publications for those
parameters will be out soon!
Amber-compatible parameters for post-translationally modified amino acids,
prepared by the Floudas group at Princeton (now Texas A&M).
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.)
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: