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XpongeCPP 0.2.15
Compatibility target: Xponge-origin 1.7.6.
Includes the public metal-patch Atom endpoint fix, deterministic AMBER improper
ordering and retained dummy bonded scaffolds described below. Complete the
synthetic CMAP and water-link test parameters and use NALA + internal ALA for
the cross-component peptide fixture. Missing production parameters still fail
strictly; no default force-field terms are introduced.
The CDK8 parameter-provenance and cross-backend ordered-improper limitations
below remain; full-engine/MD equivalence is not claimed.
Included changes
Metal patch link validation now accepts public ResidueLink Atom endpoints as
well as integer atom indices. Missing required links are still rejected; a
regression test covers both cases.
deterministic AMBER impropers (2026-10-23)
Native periodic improper matching retains original parameter slots and all
selected periodicities, with latest per-period override and stable
type/residue/local-name ambiguity resolution. Parameter lookup caches retain
slot metadata rather than occurrence-dependent permutations. Materialized FEP
endpoints continue to bypass rematching. See AMBER_IMPROPER_POLICY.md; this
does not emulate LEaP's ambiguous unit-cache ordering or change harmonic
improper definitions. No frozen input or trajectory is automatically migrated.
retained dummy bonded scaffolds (2026-10-23)
Dual construction retains opposite-branch source bond, angle and ordered
periodic torsion entities touching non-MCS atoms at both endpoints. Ghosts still
have zero LJ/charge, and endpoint NB14 uses these nonbonded states. Common-only
terms keep their physical endpoint parameters. No union-graph reparameterization
or extra cross-branch angles/torsions is performed. Ordinary modeling and the
explicit low-level one-sided soft-bond interface are unchanged.
This corrects the physical-only projection described below: auxiliary dummy
terms are part of the chosen dual-topology protocol, not unwanted physical
endpoint contamination. It is not a globally validated replacement. CDK2
historical ligand-subset tables match at seven step2 states; CDK8 still has
historical parameter-provenance and cross-backend ordered-improper discrepancies.
Do not reuse old trajectory acceptance or claim full engine/MD equivalence.