The problem hasn't been solved
Hello
I have some questions about using enzyme design application for my system.
1. I have not used RosettaMatch, but I have a rough complex structure of the enzyme with the ligand. Is it fine to use that or I need to use RosettaMatch?
My goal is to insert a linker fragment into a protein which has a chemically bound ligand. To do that, I have relaxed the structure with the chemically bound ligand and am now trying to insert the linker fragment into my protein using Remodel. The ligand is bound to a CYX residue (modified Cystein) in my protein.
Dear Sir and Madam,
I have performed a lot of attempts in order to conduct the coupled_moves docking with ligand without it protonation. I need to specify that this ligand (in his physiologically active form) has only one Hydrogen on his sulfonamide site. Nevertheless, despite the absence of any other Hydrogens both in input .params, MOL2 and PDB file, a lot of sites (sulfonamide Nitrogen with additional undesirable Hydrogen, as well as some Carbons on a benzene ring and tail) get protonated.
By the way, Ligand_Dock application also protonates all possible ligand sites.
Hello,
Can the BuriedUnsatHbonds2 filter be pushed to release? It gets called in a rosetta scripts xml included in the supplementary materials for this paper (published in 2017): DOI: 10.1126/science.aan0693
Thanks!
Hi All,
I am working on designing some symmetric structures and am currently using REF2015 + hbnet. In addition, I want to add the buried_unsatisfied_penalty. When I add this term to the score function, it works and can score 'non-symmetrized' structures just fine. However, when I try to score a structure that has been 'symmetrized' I get the following error:
File: /home/benchmark/rosetta/source/src/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.cc:637
[ ERROR ] UtilityExitException
Hi Rosetta team,
I'm trying to use step wise Monte Carlo to model RNA structure.
Here is the command I used:
Hello,
I am trying to mutate a pose with beta-amino acid residues. From what I've tried and read, it's impossible with both mutate_residue and MutateResidue mover, because they only take one letter representations of the residues. My hope is that I can figure out how to do it through packing. I'm not sure how to make it work properly.
This was just my test code to see what would work:
pose = pose_from_sequence('A'*20)
test_pose = Pose()
test_pose.assign(pose)
mutant_position = 3
Hello,
I am performing Rosetta protein-ligand docking and I added constraints both in centroid mode and high resolution mode, but the constraints are not used. I got a warning at the end of the log file saying :
protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used:
-constraints:cst_fa_file ../input_files/myconstraint.cst
-constraints:cst_file ../input_files/centroid.cst
-constraints:cst_weight 10
Dear Rosetta people,
I am trying to dock ligand, which possesses by sulfonamide NH group to the target protein with a help of coupled_moves application by the following command: