Now I’m using 2024.4,you mean the 2025-beta?
sorry my fault
Your screenshot says you are using 2021.3-bioconda. I’m suggesting you compile version 2024.4 from source, not a beta version. If you can reproduce the problem with 2024.4, that’s useful to know. I can’t see a reason why this would be happening.
Also some questions want to ask:
The Error show me some errors like this, and this PDB are from AlphaFold Database.Can i add HB3 item in aminoacids.rtp of force field？
I do not advise changing the force field residue definitions. This is a textbook case for -ignh.
Although it look like some hydrogen atoms? Most cases are HB3, HG3, HD3?
Yes, it is a hydrogen atom. Some programs and nomenclature systems use e.g. HB2 and HB3 for H atoms attached to the Cβ atom, but GROMACS and all its constituent force fields use HB1 and HB2, instead.
So can I refer to the existing parameters of HB and HB2 content in the force field file to add HB3?
Again, I do not advise editing the force field files. You don’t need to, and this is a manual and error-prone task. Please use -ignh (and solve the underlying issue first, if that is still needed - I’m not clear as to whether that has been resolved yet). The option is designed exactly for this situation.