There is a flag that I cannot recall that stops Rosetta from using ligand params from PDB and instead use the one from n:file:extra_res_fa and n:file:extra_res_cen.
What is it? I cannot find it in my notes and in the documentation.
Adding a ligand with -extra_res_fa or -extra_res_cen should turn off the loading of the PDB chemical component definitions for ligands with that same three letter code.
But if you wish to turn off the PDB CCD definitions being used generally, the option to use is `-load_PDB_components false`. Keep in mind that if you have a structure with a ligand not from the standard Rosetta set or being provided by -extra_res_fa, turning off the components loading would likely result in a program exit unless you also include the `-ignore_unrecognized_res` flag.
Thank you, yet again.
Uhm. In my hands it opts for PDB_components before going for extra_res params.
Don't get me wrong, I really like it —most of the time. I remember switching from 3.6 to 3.7 (? when the PDB CDD denifitions were there added) and I didn't have to worry about silly things like phosphates and their kin.