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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Received on Mon Sep 08 2025 - 09:00:02 PDT
