Description:
bio-forge ≤0.4.0 treats every N-terminal residue as a primary amine in ops::hydro::construct_n_term_hydrogens, ignoring that PRO's backbone nitrogen is a secondary amine (N–CA + N–CD). This over-places one hydrogen and omits the N–CD direction constraint, producing an invalid N coordination geometry. dreid-typer derives DREIDING atom types from degree and bond angles; the spurious hydrogen inflates the nitrogen degree and pushes angles outside the sp³ window, failing atom-type assignment and halting parameterization. Fixed in bio-forge v0.4.1.
Tasks:
Description:
bio-forge ≤0.4.0treats every N-terminal residue as a primary amine inops::hydro::construct_n_term_hydrogens, ignoring that PRO's backbone nitrogen is a secondary amine (N–CA + N–CD). This over-places one hydrogen and omits the N–CD direction constraint, producing an invalid N coordination geometry.dreid-typerderives DREIDING atom types from degree and bond angles; the spurious hydrogen inflates the nitrogen degree and pushes angles outside the sp³ window, failing atom-type assignment and halting parameterization. Fixed inbio-forgev0.4.1.Tasks:
bio-forgeto0.4.1