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.
Are you doing this with Rosetta++ or Rosetta3? (This is the Rosetta++ section of the forums.) The path you give indicates you're probably using Rosetta3 (3.4 or 3.5 perhaps?).
For new work (i.e. if you're not trying to replicate/match previous work done in Rosetta++), I'd highly recommend using Rosetta3. Not much development work has been done recently on Rosetta++.
If you're using Rosetta3, see my response to your question over there ( https://www.rosettacommons.org/node/3618 ).
sorry，I have got the correct answer in Rosetta3 section in the forum. The administrator can delete my topic in Rosetta++ now.