I tried adding the patch files pro_hydroxylated_case21.txt and pro_hydroxylated_case2.txt to
../rosetta_database/chemical/residue_type_sets/centroid directory and also adding the file names to the patches.txt file.
I still get the above error.
Example of patch file:
NAME pro_hydroxylated_case2
TYPES HYDROXYLATION
## general requirements for this patch
BEGIN_SELECTOR
PROPERTY PROTEIN
AA PRO
NOT VARIANT_TYPE HYDROXYLATION
END_SELECTOR
## now we search for a case that matches the residue, take the first one
## so put generic case last
BEGIN_CASE ### THE GENERAL CASE ##########################################
SET_IO_STRING HYP P
END_CASE
Post Situation:
If I wasn't clear, the switch from centroid - to - residue-type-set fails.
See what happens if you put your structure through score_jd2 with the -out:pdb flag on. What does the output copy of the PDB (specifically, the hydroxyproline) look like?
Also, you have a typo in your listing of the files - it's case 1 and case 2, not case 21 and case 2. I assume this is an innocent typo in the message board posting, but if your files are really named that way it might cause a problem.