C-terminus protonation using PDB2GMX

User discussions
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1

GROMACS version: 2020.4
GROMACS modification: Yes/No

Hello,
I am using the AMBER99SB force field for peptide simulations. Using PDB2GMX, I want to protonate the C-terminus. I know that the -ter flag does not work for AMBER. I tried to prefix the residue names with N and C for N-term and C-term, respectively, but it did not work. How can I protonate the C-terminus of the peptide using PDB2GMX to get an .itp file?

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I think there is no direct method because AMBER forcefield does not define this capping method. Only to change the forcefiele or manually supplement .rtp and .r2b file.
(I used to have the same problem and did not solve in the end, or someone else might have better method :3)

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I used to edit the pdb file manually.