How do you use two patches simulataneously with ab initio folding?

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 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?

I dug into it more and replonly doesn’t make named patches, so Ray’s input is definitely needed…

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.