Protein Force Fields
For a full description of the force fields and how to load them, please read Chapter 3 of the Amber Reference Manual.
field is the most current protein force field.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.
The ff19SB force field contains amino-acid specific backbone parameters. ff19SB pairs best with the more accurate OPC water model. Note: This adds up to 33% computational time over the ff14SBonlysc/OPC3 and ff14SB/TIP3P combinations but is expected to be more accurate.
Ref: C. Tian; K. Kasavajhala; K. Belfon; L. Raguette; H. Huang; A. Migues; J. Bickel; Y. Wang; J. Pincay; Q. Wu; C. Simmerling. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. J. Chem. Theory Comput., 2020, 16, 528–552.
- In the ff14SBonlysc force field,
the side-chain dihedral parameters were fit to quantum mechanical data for each amino acid.
ff14SBonlysc is the same
model as ff14SB but without the empirical backbone corrections for TIP3P.
For simulations in implicit solvent (igb=8), ff14SBonlysc is best.
If you want a 3-point water model to minimize computational cost, this is a good choice
The ff14SB force
is intended for use with the TIP3P water model.
Backbone parameters were based upon alanine and glycine, including a TIP3P-specific correction to the backbone parameters.
Specialized Protein Force Fields
ff15ipq-m (protein mimetics)
- The ff15ipq-m force field is an expansion of the ff15ipq force field that enables the modeling of protein mimetics containing artificial backbone units that belong any of the following four classes: D-alpha residues, beta3 residues, C-alpha-methylated alpha residue Aib, and cyclic beta residues.
ff15ipq (including fluorinated aromatic amino acids)
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 field also includes parameters for fluorinated aromatic amino acids.