Reply To: I am a beginner in rosetta software and need help to build params file

[Anonymous]

The Rosetta database has params files for some metal ions already (see minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions), including both iron III (residue name FE) and iron II (residue name FE2). The “trick” to make monoatomic ions work is to put in virtual atoms such that the metal ion can be oriented in space. molfile_to_params.py isn’t really set up to do this, so if you want to make a metal ion parameter file, your best bet is to copy one of the existing files and tweak it appropriately. Note that if you want to use a residue that’s already in the database, you don’t have to make a new params file, or even specify the existing one with -extra_res_fa. If you use the appropriate residue name, Rosetta should be able to find the params file in the database. (So for matching, a “-match:lig_name FE” without the -extra_res_fa should be sufficient.)

I note that your residue is listed as heme – note that if you’re trying to place a metal ion in combination with another small molecule (an iron coordinated heme, for example), your best bet is to treat the entire complex as a single ligand. All you need to do is add “dummy” single bonds so that the entire “residue” is connected by bonds, and then pass that mol file through molfile_to_params.py. (Note that you don’t need the virtual atoms then, as the other atoms in the residue serve to orient it.)

Finally, keep in mind that the parametrization of metal atoms in Rosetta is not as developed as the standard protein atoms (most importantly, orbital geometry isn’t considered). Matching is purely geometric, so you should be fine, but I recommend you be a bit skeptical of the results coming out of energy minimization or design runs. That is, check that the results make sense chemically.

-Rocco