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How to add uncommon metal elements into Rosetta and make it recognizable?

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How to add uncommon metal elements into Rosetta and make it recognizable?

HI everyone, I want to RosettaMatch to introduce a ligand into a scaffold protein, but the ligand contains uncommon metals like Rh, I am afraid Rh is not recognizable like Fe by Rosetta. 

So I want to ask about how to add a new metal element to Rosetta, and how many files should I edit to make sure it's done? As far as I know, maybe I have to edit atom_type_sets and residue_types sets under database/chemical/, but more specifically, I have no idea.

Any suggestions would help!  And thanks for you time and effort.

Post Situation: 
Thu, 2023-02-09 00:08

First of all: what are the valencies of the metals in the ligand? In any case, the only approach that I'm aware of is to build an additional residue parameter file (.params).,What%20is%20a%20Params%20File,file%20associated%20with%20that%20residue.

Thu, 2023-02-09 05:14

The valencies if metals are +3 in the ligand. So, I just need to add an residue params file?

Thu, 2023-02-09 22:08

I would start by modifying another metal ion already present in Rosetta, like Fe3+ (Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/FE.params). Copy the params file and edit the properties to match your metal ion. You may also need to look into other database files to edit items like the vdW radius, etc. Look for these kinds of files in the subdirectories of main/database/chemical. I would expect Rosetta to error out if it looks for information in the database and can't find it. Add this information (or fudge it) until Rosetta runs successfully.

Some metal ion-specific code in Rosetta sets up constraints for metal interactions. It uses the option -auto_setup_metal_constraints (or similar). Seek this out and understand how you would need to make additions for your specific metal ions and the expected valencies (or set up a constraint system externally).

Good luck!

Fri, 2023-02-10 08:21

Thank you very much! That helps a lot!

Sat, 2023-02-11 00:44