I am trying to run a point mutant scan on a GFP variant. I created a CRO.param file for the GFP chromophore using InteractiveRosetta. I have attached the CRO.param file as a .txt file. First, I tried putting the CRO.param file in the rosetta database in the l-caa folder in residue_types. I added a line within residue_types.txt as well to include the CRO.param file. I then tried to run the point mutant scan - input here:
/Path/rosetta_bin_mac_2016.10.58534_bundle/main/source/bin/pmut_scan_parallel.macosclangrelease -database /Path/rosetta_bin_mac_2016.10.58534_bundle/main/database -s /Path/rosetta_bin_mac_2016.10.58534_bundle/pdb/GFP.pdb -output_mutant_structures -DDG_cutoff 0 -ex1 -ex2 -extrachi_cutoff 1 -use_input_sc -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core
I received an error shown here:
ERROR: Failed to apply a PatchOperation to CRO
ERROR:: Exit from: src/core/chemical/Patch.cc line: 339
I then tried to use the -extra_res_fa /Path/CRO.param tag followed by my path to the CRO.param file (after removing the CRO.param file from the database and placing it elsewhere). However, this time, I received this error:
ERROR: name_map_.find( residue_type->name() ) == name_map_.end()
ERROR:: Exit from: src/core/chemical/ResidueTypeSetCache.cc line: 57
Is there something obvious that I am missing here or a better way to go about doing this? I have also uploaded the pdb file as a .txt file. Thank you for your help.
One issue you're running into is that there's a TER card right before your CRO residue, which means that Rosetta is trying to find an N-terminus variant of the CRO residue. Since the CRO isn't a standard amino acid, which means that Rosetta is having difficulty making that version. If you remove the TER card from the input PDB, you should get rid of the "Failed to apply a PatchOperation" message.
The other issue is due to a slightly different way Rosetta is not figuring out which residues are appropriate to load. Specifically, your CRO.parametrs file doesn't have a PROPERTIES line. If you add "PROPERTIES PROTEIN L_AA" to your params file, it should work.
Thank you! The "PROPERTIES PROTEIN L_AA" line in the params file worked perfectly.