it might depend on which force field and libraries you are loading. In
Amber, you normally convert an N-terminal (or C-) residue name to start
with "N" (ALA changes to NALA). Then, you need to have library files
describing that version. It's entirely possible that whoever developed the
ASH library that you are using did not make the N- and C- terminal
versions, and also that Leap does not automatically map ASH to a terminal
residue name. This would lead to you seeing it as just the "internal" ASH
that was in the library file.
So - you need an NASH library, and then may need to rename it in the input
PDB rather than counting on Leap to do that for you.
On Mon, Sep 8, 2025 at 11:37 AM Cherry, Kendall via AMBER <amber.ambermd.org>
wrote:
> Hello Amber community,
>
> Has anyone used ASH residues at terminal positions before? My protein has
> an N-terminal Asp and I am trying to simulate it at low pH, so I want that
> Asp to be protonated. When I switch ASP to ASH before passing it into
> tleap, I noticed that the N-terminal amine only has a single proton on it,
> as if it were part of a backbone amide. It has a negative charge when I
> look at it using desc within tleap. I am curious if there are parameters
> for this residue somewhere, or if I should create it as a nonstandard
> residue.
>
> Thank you,
> Kendall Cherry
>
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