I tried to use replonly and phosphorylation patches together but couldn't get the simulation to work. The program only recognizes the 1st declared patch.
Try out:level instead of run:level for the big list o' patches.
Looking at the code directly, it seems to me they should combine fine. Did you try both permutations?
I've cc'ed one of the devs about reponly.
I dug into it more and replonly doesn't make named patches, so Ray's input is definitely needed...
Yes, I did. Same problem.
I wonder did you get the phosphorylated patch work stand alone? The ser_phosphorylated.txt cannot be called by using -patch_selectors since it doesn't has CMDLINE_SELECTOR inside that. So the question now is how to use ser_phophorylated.txt patch. Anyone?
Have you tested whether your pdb has the ser_phosphorylated.txt patch created? Also, since this ser_phosphorylated.txt patch is to be read by Rosetta in default, you don't need to specify that using -patch_selectors as you used for replonly.