Reply To: Using Patches in Rosetta

[Anonymous]

A couple of things:

1) I failed to check that the formatting didn’t break – all the special residues are supposed to be surrounded by square brackets, which the formatting turned into underscores (perhaps you knew this?)

2) I forgot about centroid for abinitio. The sulfur won’t make any difference in centroid mode (it’s not fine grained enough), but I see why it was giving you problems. You should try creating a centroid tyrosine sulfate patch. Then maybe it will do centroid with tyrosine, and then convert it to fullatom centroid when it switches into fullatom mode. I think it would look something like this:

~~~~~~~~~~~~~~~~~~~begin~~~~~~~~~~~~~~~~~~~~~~`

NAME sulfated
TYPES SULFATION

## general requirements for this patch
## require protein, ignore anything that’s already nterm patched:

BEGIN_SELECTOR
PROPERTY PROTEIN
AA TYR
NOT VARIANT_TYPE PHOSPHORYLATION ## Just in case
NOT VARIANT_TYPE SULFATION
NOT VARIANT_TYPE PROTONATED
NOT VARIANT_TYPE DEPROTONATED
END_SELECTOR

BEGIN_CASE ### THE GENERAL CASE ##########################################

ADD_PROPERTY CHARGED ## For the sulfate group

END_CASE

~~~~~~~~~~~~~~~~~~~~~~~end~~~~~~~~~~~~~~~~~~~~“`

3) Just knowing that there’s a segfault is not enough for me to diagnose, sorry!