[AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ?

From: Yen Nguyen <ynguyen3.gmu.edu>
Date: Thu, 18 Nov 2021 19:47:43 +0000

I've been searching for a way to build a peptide sequence with C and N terminal modifications (C -terminal = amidated Lys, N-terminal = acetylated Trp in tleap (AMBER), but I couldn't find a way to make/add an amidated Lys residue at the C-terminal. AMBER has the code ACE for acetylated residues, but I don't know if it has a code for amide terminals?
I'm using amber 18 and the protein forcefield leaprc.protein.ff14SBonlysc , which has the following parameter files
I have a pdb file of the peptide, but it looks like AMBER doesn't utilize pdb files to create prmtop and coordinate files for my peptide.
I'd greatly appreciate any help. Thank you!

Yen Nguyen
Graduate Research Assistant
George Mason University
Department of Chemistry and Biochemistry
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Received on Thu Nov 18 2021 - 12:00:05 PST
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