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Is there a scripted tool to add neutral terminal caps (e.g. NME, ACE) to peptide chains for use with AMBER forcefields?

I have a range of systems consisting of multiple peptide chains, some of which are one residue (i.e. single amino acids), which I'd like to analyse using molecular dynamics and AMBER-flavour forcefields. Each peptide fragment is a connected chain with unique chain IDs, separated by TER records.

Is there a scripted or automated tool out there to add neutral terminal caps - e.g. n-methyl (NME) and methyl-acetate (ACE)?

Some options that work well but don't seem to help with this specifically:

  • tleap: requires manual editing to change the residue name of one atom at the end of each chain into NME and ACE. After this, tleap can add missing atoms, but the key step is manual
  • pdbfixer: can add charged terminal caps, but not NME/ACE
  • pdb2gmx: does not add NME/ACE; requires manual editing of the PDB file
  • CHARMM-GUI: not scripted/automated
  • HTMD / Maestro: apparently these would work but I don't have a license!