CT2 amidation on C-terminus not updating on topology file - Charmm36-jul2022.ff

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question: I am trying to amidate the C-terminus using the CT2 patch. However, it doesn’t look like my topology file is updated even after I add the CT2. Please assist.
Thank you.

2

delete any NH2 or from COOH the OH in the pdb (you have to have a -CO at tyhe C-term) and let pdb2gmx to add the CT2

3

I do not have any NH2 or COOH in the pdb as that was giving me errors. I am using the CT2 option which seems to not be updating my topology file.