Broken Protein after Solvation

GROMACS version: 2018.3
GROMACS modification: No

I am running MD simulation for a protein.
A simulation box was created, and the protein was solvated. But when I used Amber99SB-ILDN, side chain of C-terminus residue seems detached and doesn’t appear as a part of the protein on VMD.

But the structure looks fine when I use Gromos54a7. Has anyone experienced this kind of issue?

Thank you.

The protein is fine, see

Plus could also be due to VMD not knowing which bonds should be there, it guesses based on distance, see

Thank you for the reply. I guess I will just try moving onto the next step, and see if something weird happens.

Another question has to do with creating .itp file for my ligand.
I use ATB web server to create one for Gromos forcefield, but not sure about what to use for Amber99SB-ILDN. I found that I should use acpype, but not quite sure how to set it up and use it. Some links to the tutorial do not exist anymore.

Any help will be appreciated.