Hi I have tried using -ter but the result is like this:
Program: gmx pdb2gmx, version 2023.2-Homebrew
charmm36-jul2022.ff and -ter
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 870)
Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS.
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
I would like to know how to fix it.