Hotfix/pdb2amber neutralization

[David-Araripe]

Summary

This PR hardens protein preparation in two areas:

1. It normalizes amino-acid atom names and protonation-state geometry to the AMBER14sb conventions expected by pdb2amber/qprep.
2. It makes out-of-sphere neutralization follow Q's force-field-specific charge-group rules while retaining the 3 Å outer SCAAS-layer default used by the benchmark preparation protocol.

Motivation

Input structures from different preparation tools can use different atom-numbering conventions, particularly for protonated carboxylates, neutral arginine/lysine, methyl hydrogens, and terminal oxygens. Some of these differences previously produced duplicate or incorrectly bonded atom identities after renaming.

Boundary neutralization also needs to use the same inclusion/exclusion reference as Q. A residue centroid or a single hard-coded atom does not reproduce Q consistently across force fields because AMBER and OPLS have different charge-group declarations (see FF/*.lib).

The need for these changes was flagged by @goodstudyqaq who SHAKE failures on the GPU kernel. The culprit was incorrect atom naming in the benchmarking repository, where a hydrogen that should belong to OE2 was incorrectly attached to OE1. This wasn't picked up in fortran as SHAKE allowed very high coordinate correction there.

Changes

PDB-to-AMBER atom normalization

• Normalize GLH/ASH acidic hydrogen and oxygen identities from geometry without moving coordinates.
• Normalize neutral ARN terminal nitrogen/hydrogen identities from their bonding geometry.
• Correct numbered methyl-hydrogen mappings for ALA, VAL, and MET.
• Normalize neutral LYN hydrogens to AMBER14sb HZ2/HZ3 names.
• Handle protonated terminal-oxygen aliases and produce the expected charged C terminus.
• Validate explicit backbone amide H–N distances.
• Reject unresolved duplicate atom names rather than allowing residue nesting to split them silently.

Force-field-aware boundary neutralization

• Preserve the default 3 Å neutralization layer: groups at or beyond sphere radius - 3 Å are neutralized.
• Read charge groups from the selected Q .lib file and switch_atoms from its .prm options.
• Match Q's boundary reference:
  • AMBER (switch_atoms off): geometric center of the formal charge group.
  • OPLS (switch_atoms on): first atom of the explicit formal charge group.
• Derive atoms removed during charged-to-neutral conversion from the selected force-field templates.
• Handle nonstandard OPLS terminal residue names through template charge and atom-set matching.
• Detect boundary-crossing salt bridges using charged heavy-atom distances and neutralize the included partner together with the excluded residue.
• Report the force field, boundary policy, modifications, salt bridges, terminal conversions, and full template-based charges in the returned statistics.
• Fail explicitly for CHARMM until equivalent force-field-sensitive neutralization is implemented.

Force-field parsing

• Extend parse_lib() to retain [charge_groups] and residue names containing punctuation, such as NAR+.
• Add parse_prm_options() for reading options such as switch_atoms.

Testing

PYTHONPATH="$PWD/src" python -m pytest -q \
  test/qligfep/test_pdb_to_amber.py \
  test/qligfep/test_qprep_cli.py \
  test/qligfep/test_io.py