Parameters

The TOPO force-field constants are defined in topo.parameters.model_parameters. The "topo" model provides:

  • Per-residue properties — mass (amu), radii (excluded-volume radius, nm), and charge (e) for each residue type. Only ASP/GLU (−1) and ARG/LYS (+1) are charged; all others are neutral. The full table is in The TOPO model: theory and force field.

  • Bonded constants — bond_length_protein = 0.381 nm, bond_force_constant = 20920 kJ mol-1 nm-2, and the bonded_exclusions_index = 2 rule (pairs two or fewer bonds apart — i.e. 1–2 bonded and 1–3 angle neighbours — are excluded from the non-bonded forces).

  • Sequence-dependent dihedral parameters — periodic-torsion phases and force constants keyed by the two central residues of each dihedral, loaded from topo/parameters/data/dihedral_params.csv by topo.parameters.dihedral.load_dihedral_params() (Karanicolas–Brooks-style values, scaled by a 0.756 calibration factor).

The sidechain–sidechain contact energies use the Betancourt–Thirumalai (BT) residue-pair potential in topo/parameters/data/bt_potential.csv (loaded by topo.utils.nonbonded.load_bt_potential()); see Structure-based contacts — the heart of the model.

See also

The TOPO model: theory and force field for the functional forms that consume these constants.

API reference

Dictionary contains parameters for TOPO model (topology-based coarse-grained model for folded proteins).

First-level key is the model name. Currently only the “topo” model is defined:

  • topo: topology-based / structure-based model for globular (folded) proteins, with residue parameters (mass, Rmin_2, charge) and non-bonded interaction matrices.

Rmin_2 is the collision radius Rmin/2 (nm): half the pair distance of minimum non-bonded energy. Pairs combine by the sum rule R_ij = Rmin_2_i + Rmin_2_j (O’Brien’s convention). (Field was named radii before; renamed for clarity – it was always an Rmin/2, never a diameter or a Lennard-Jones sigma.)

IMPORTANT – what these Rmin_2 values are used for. They are the fixed per-type radii for rigid scenery beads: the ribosome’s RNA (P/R/BR) and ribosomal-protein (per-AA) beads, read by topo.csp.ribosome.load_ribosome(). A mobile protein chain (the nascent chain, or a folded-protein simulation) does not use these: its excluded-volume Rmin/2 is per-residue and structure-derived (Karanicolas-Brooks, from build_nonbonded_interaction), so the same residue name (e.g. ALA) has a K-B value in a nascent chain but this fixed table value in a ribosomal protein. This mirrors O’Brien, who separates the two by atom type (nascent A_i vs ribosomal S<aa>) while keeping standard residue names. The protein Rmin_2 below are O’Brien’s per-AA sidechain values (his ribosome .prm S<aa> types == the topo OBRIEN_SC_RMIN_2_NM table).

ivar parameters:

Dictionary of model parameters, keyed by model name (e.g. “topo”).

vartype parameters:

dict

topo.parameters.dihedral.load_dihedral_params()[source]

Load dihedral_params from topo/parameters/data/dihedral_params.csv.