I'm sorry if this is an old thread, I did find other forums dealing with unrecognized atoms but in those threads my problem was not resolved. I am trying to follow the rosetta_CM tutorial and I got through the setup_rosetta_CM.py script and it generated the .xml file which I checked and it looked good. However, when I run the hybridized steps using rosetta scripts I get this error:
ERROR: unrecognized atom_type_name 'CS'
The unfortunate thing is I can't find any CS atoms or CS (using the find function in vim) in my PDB
The second line says this:
I'm pretty novice at coding but I tried to follow it and there is a line that says 'ignore white space' with a code line that looks like it removes spaces. I had an idea that maybe it trimmed wo much and combined a C with a S from a SER which I do have in my PDB but this is very unlikely as I've done quite a bit of modeling without this issue. Although this is my first time using 3.10, the last time I used rosetta was with 3.6.
I've attached the PDB that the setup python script created and the spacing looks normal and in line. Please let me know if you need more information to try to troubleshoot this problem.