charmm36mut force field failed with Fatal error: Atom type ON2 (residue TPO) not found in atomtype database

[Lyn-666]

Hi, thanks for your amazing work. I try to pmx to create hybrid topology and protein files. I used charmm36mut force field to generate mutate protein ( works well). after that, I used pdb2gmx to create hybrid topology files with charmm36mut force field, but it shows:

Fatal error:
Atom type ON2 (residue TPO) not found in atomtype database

It works well when i input the same force field and protein file on the website server, and it also works if i change the force field into charmm22 on the terminal command.

I think the charmm36 force field has something wrong, but I have no idea how to fix this problem as i am a new student here. could you please help me fix it? thanks!

[SSNbehera]

Hi,
It seems like a similar issue as discussed here.

You could run your pdb file through fix_residue_names.py and hydrogen_atom_renaming.py, present here, before doing pdb2gmx.

Best,
Sudarshan

[Lyn-666]

Thanks very much