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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!
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  • $\begingroup$ I’m rusty with this but I had a script programmatically create input for tleap and I believe ACE was right before our first residue. I believe we would have to create a timer between inputs because tleap would start to have issues if input was made all at once. Would something like this be feasible? I’ll see what I can pull off my research computer. $\endgroup$
    – Melanie Shebel
    Commented Aug 12, 2022 at 2:08
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    $\begingroup$ In Ruby. No docs, sorry. Our docs were taken down years ago when our lab closed. Mine has ACE and NME. gist.github.com/MelanieS/74b578ac2d2a0dd50372 $\endgroup$
    – Melanie Shebel
    Commented Aug 12, 2022 at 2:14

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you can try use pymol to do this.

use Ctrl+middle click to pick an atom,e.g.the N atom of first residue,

then >>Build>>adresidue>>Ace. same as NME.

and save the new structure.

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for what it's worth, i made a script that automates this with tleap but it also involves a truncation step (distance based): https://github.com/camattelaer/AMBER-TruncAndCap

It's written in bash, so you can easily modify it to just use an already truncated model, or just an entire system.

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