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symmetric design w/ hbnet and unsatisfied_buried_penalty score terms

Category:
Design

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

Post Situation:

RNA modeling with step wise Monte Carlo error

Category:
Structure prediction

Hi Rosetta team,

I'm trying to use step wise Monte Carlo to model RNA structure.

Here is the command I used:

Post Situation:

Mutate residue with NCAA

Category:
PyRosetta

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

Post Situation:

constraint are not imposed during protein-ligand docking

Category:
Constraints

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

Post Situation:

Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms

Category:
Docking
Small Molecules
Chemically Modified Residues

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:

Post Situation:

Can I believe the antibody design result?

Category:
Design

I am trying to do antibody design with the  RosettaAntibodyDesign, but some of my colleagues told me that they fell to obtain successful designers with the  RosettaAntibodyDesign (RAbD). They ran the RosettaAntibodyDesign on the crystal structure of an ab-ag complex with a dG_seperate of about -20 REU, and got some designers with dG_seperate of about -40 REU. However, they did experiments including ELISA and SPR and found that these antibody designers did not bind to the antigen at all!

Post Situation:

Constraints residues in different chain in protein-protein docking

Category:
Docking

Hello,

I want to dock two proteins. I have some constraints between residues of different chain (here chain A and B).

For eaxmple:

For residues number 15 of chain A, and residue number 271 of chain B, I have the following information:

The minimum distance between residues is 0, and the maximum distance is 6.

How can I add constrain for something like this case (I mean when residues are in different chain)? How can I specify that residues are in diffrent chain?

Post Situation:

polymer docking using rosetta scripts

Category:
Docking

Hi  My name is  Jong hui Hong

I'm trying to dock the ligand which has 5 chemical linked via covalent bond( ACE-UB4-DPP-GLY-GVE) using Rosetta-Scripts

I changed ligand residue name into PRD and made conformer using obabel , made paramter file using molfile_to_params.py without any problem

but when I run docking using  rosetta_scripts.linuxgccrelease

I got the following error

Post Situation:

Extending Pyrosetta toturials for docking by adding constraints

Category:
Docking

Hello,

I followed pyrosetta tutorials for docking.  I did something like the following:

scorefxn_low = create_score_function("interchain_cen")
jd = PyJobDistributor("output", 100, scorefxn_low)
while not jd.job_complete:
cen_pose.assign(starting_cen_pose)
dock_lowres.apply(cen_pose)
jd.output_decoy(cen_pose)

Then, I selected the candiddate with lowest score.

Post Situation:

Error: in membrane docking : Cannot split pose by membrane jump! Quitting...

Category:
Docking

I'm trying to run the demo files of RosettaMP and it fails in the last docking step. We were able to prepack the files normally , but the last command throws error:

core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set.  Created 62 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 0.016093 seconds.

protocols.docking.DockingProtocol: FOLD_TREE  EDGE 81 1 1  EDGE 1 40 -1  EDGE 1 61 2  EDGE 61 80 -1  EDGE 61 41 -1

Post Situation: