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?
The protein forcefield I'm using is 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!