I think you're looking for the "NHE" residue.
it should work ok if your pdb file has the matching residue and atom names.
if not, you can rename them following the info below:
NHE INT 1
NH2 ENDING GROUP
4 N N M 3 2 1 1.335 116.600 180.000 -0.46300
5 HN1 H E 4 3 2 1.010 119.800 0.000 0.23150
6 HN2 H E 4 3 2 1.010 119.800 180.000 0.23150
On Thu, Nov 18, 2021 at 2:48 PM Yen Nguyen <ynguyen3.gmu.edu> wrote:
> Hello,
> 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
> /amber20/dat/leap/parm/parm10.dat
> frcmod.ff14SB
> frcmod.ff99SB14
> 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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>
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Received on Thu Nov 18 2021 - 12:00:06 PST
