Enum: ProteinPotentialName

Force fields used to parametrize amino acids in proteins in a simulation.

URI: https://CCPBioSim.ac.uk/biosim-schema/ProteinPotentialName

Permissible Values

Value	Meaning	Description
ff19SB	None	As of Amber24, ff19SB is the latest model of SB protein force fields and has …
ff99SB	None	All-atom molecular mechanics force field specifically designed to simulate pr…
ff99SB-ILDN	None	Refined extension of the foundational Amber ff99SB model, specifically optimi…
ff99SB-disp	None	Optimized by D
ff14SB	None	Older version of the SB protein force fields that utilizes uncoupled phi/psi …
ff14SBonlysc	None	Includes the ff99SB backbone parameters with updated side chain (sc) paramete…
ff15ipq	None	Continues the development begun with the ff14ipq force field for proteins, bu…
fb15	None	The force balance (fb) protein force field that can be used for protein-water…
ff03	None	A modified version of ff99, where charges are derived from quantum calculatio…
ff03ua	None	The united-atom counterpart of ff03, which uses the dame charging scheme as f…
phosaa10	None	Force field for phosphorylated amino acids
phosaa14SB	None	Force field for phosphorylated amino acids with ff14SB
phosaa19SB	None	Force field for phosphorylated amino acids with ff19SB
ff14SB_modAA	None	Force field with ff14SB for modified amino acids like selenomethionine, cyano…
ff19SB_modAA	None	Force field with ff19SB for modified amino acids like selenomethionine, cyano…

Slots

Name	Description
protein_potential_name	Force field used to describe proteins

Identifier and Mapping Information

Schema Source

• from schema: https://CCPBioSim.ac.uk/biosim-schema/

LinkML Source

name: ProteinPotentialName
description: Force fields used to parametrize amino acids in proteins in a simulation.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  ff19SB:
    text: ff19SB
    description: As of Amber24, ff19SB is the latest model of SB protein force fields
      and has shown to improve amino acid-dependent properties such as helical propensities
      and reproduces the differences in amino acid-specific PDB Ramachandran maps.
  ff99SB:
    text: ff99SB
    description: All-atom molecular mechanics force field specifically designed to
      simulate proteins and peptides
  ff99SB-ILDN:
    text: ff99SB-ILDN
    description: Refined extension of the foundational Amber ff99SB model, specifically
      optimized to fix errors in side-chain rotamer distributions.
  ff99SB-disp:
    text: ff99SB-disp
    description: Optimized by D.E. Shaw Research to accurately simulate both folded,
      structured proteins and intrinsically disordered proteins (IDPs) or highly flexible
      peptide states.
  ff14SB:
    text: ff14SB
    description: Older version of the SB protein force fields that utilizes uncoupled
      phi/psi dihedral parameters for the protein backbone, and every amino acid except
      for glycine used the backbone dihedral parameters fit using alanine.
  ff14SBonlysc:
    text: ff14SBonlysc
    description: Includes the ff99SB backbone parameters with updated side chain (sc)
      parameters that were derived from ab initio quantum mechanics calculations.
  ff15ipq:
    text: ff15ipq
    description: Continues the development begun with the ff14ipq force field for
      proteins, but offers new parameter choices, data fitting and validation.
  fb15:
    text: fb15
    description: The force balance (fb) protein force field that can be used for protein-water
      simulations.
  ff03:
    text: ff03
    description: A modified version of ff99, where charges are derived from quantum
      calculations that ise a continuum dielectric to mimic solvent polarization.
  ff03ua:
    text: ff03ua
    description: The united-atom counterpart of ff03, which uses the dame charging
      scheme as ff03, but the aliphatic hydrogen atoms on all amino acid side-chains
      are united to their corresponding carbon atoms.
  phosaa10:
    text: phosaa10
    description: Force field for phosphorylated amino acids.
  phosaa14SB:
    text: phosaa14SB
    description: Force field for phosphorylated amino acids with ff14SB.
  phosaa19SB:
    text: phosaa19SB
    description: Force field for phosphorylated amino acids with ff19SB.
  ff14SB_modAA:
    text: ff14SB_modAA
    description: Force field with ff14SB for modified amino acids like selenomethionine,
      cyano-phenylalanine, and azido-phenylalanine, acetylated lysine and for the
      nitroxide spin-label methanesulfonothioate (MTSL).
  ff19SB_modAA:
    text: ff19SB_modAA
    description: Force field with ff19SB for modified amino acids like selenomethionine,
      cyano-phenylalanine, and azido-phenylalanine, acetylated lysine and for the
      nitroxide spin-label methanesulfonothioate (MTSL).