- This topic has 2 replies, 2 voices, and was last updated 9 years, 8 months ago by Anonymous.
March 25, 2014 at 3:34 am #1858Anonymous
I’m using enzyme design to redesign a enzyme, and encountering a tough problem for me.
In the catalytic site, there is a protonated ASP, and a .cst file need to be given to constraint -OH of ASP and ligand.
Although I find the parameters of protonation state of ASP (ASP_P1.params or ASP_P2.params file) in the installation directory(…/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states),
the 3 letter abbreviation of protonated ASP is also ASP, so I don’t know how to inform the rosetta to recognize the ASPH.
I think a simple setting could sovle the problem, but it puzzuled me for a long time.Can someone give me a solution for this?
Thanks in advance for your suggestions.
March 25, 2014 at 3:00 pm #9921Anonymous
In Rosetta3 (or at least later versions of it), we do have protonation states in the database directory, but they’re only loaded if the “-pH:pH_mode” commandline flag is given. But you probably don’t want to enable that, as that would allow the protonated variant at *all* positions of the protein, rather than just the position you’re interested in. Instead, I’d recommend making a “new” params file used for just your location by copying the existing protonated variants, choosing a non-ASP three letter code, altering the IO_STRING line to use the new three letter code, changing the AA line from ASP to UNK, and then, if you’re using Rosetta3.5, adding a “ROTAMER_AA ASP” line to the file. Then it’s simply a matter of including the new params file with the -extra_res_fa flag, and using the new three letter code instead of ASP at the appropriate locations. (e.g. in the constraint file, and in the REMARK lines and ATOM records of the PDB file).
The other alternative is to simply ignore the proton when doing your modeling. The ASP-ligand interaction is being enforced by the constraints, so you probably don’t need the proton to be actually present during modeling in order for things to work out decently. (If you currently have the constraints written based on the proton, you can always re-write them based on heavy atoms — using heavy atoms for your constraints is something of the recommended way of doing things, anyway.) If your constraints are set up correctly, the presence/absence of the proton will likely not make too much of an issue in most Rosetta runs.
March 26, 2014 at 6:06 am #9924Anonymous
Thank you very much! After reading your suggestion, I have a new understanding of rosetta.
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