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I’m a noob in rosetta modelling. I need to model my protein at low pH, i.e. with protonated Asp and Glu residues. How should I setup the simulation(ab initio and relax)?
I found there are residue type files for fullatom protonated Asp and Glu in rosetta_source directory, but I don’t know how to use them:(
Thank you very much,
There are two flags one can add to activate those protonation states. It is unclear what changes need to be made to the scorefunction in general (I mean the science is unclear), so it’s pretty experimental. Please see this post: http://www.rosettacommons.org/content/mitochondria-protein-modeling#comment-5435