You are here

Unsolved

The problem hasn't been solved

Usage of the TaskOperations "RestrictToCDRsAndNeighbors"

Category: 
Design

Hi, I would like to include the TaskOperations "RestrictToCDRsAndNeighbors" in my xml file which is to design the CDR in an antibody-antigen interface.

However, I do not know what to put as options under the arguments "numbering_scheme" and "cdr_definition"

From the manual, the explanations are

Post Situation: 

Bound Ligand Protein-Protein Docking

Category: 
Docking

Hi,

I am trying to run on the Rosie server some docking2 tests with bound ligand in each protein. In fact, I would like to explore a situation of how two protein interacts with each other with bound ligand. However, when I launch jobs with ligand coordinates at its final site included in the PDB, the simulation fails and I receive an error message.

I, therefore, write to ask whether is it possible to do on ROSIE server?

I thank you all in advance,

Haresh

Post Situation: 

ERROR: Specified chain does not exist.

Category: 
Docking

Hello,

I am using already preinstalled software Rosetta 3.10 on ComputeCanada (CCDB). I have run demos tutorial of protein-protein docking, was running successfully. Later, I have submitted own protein-protein docking job. I got an error(see below). Please, I need to help solve this problem.

 

--------------------------------------------------------------------

[ajanihar@gra-login3 input_files]$ rosetta_scripts.mpi.linuxiccrelease @docking_full.options -parser:protocol docking_full.xml -out:suffix _full -nstruct 5

Post Situation: 

intrensic disrodered proteins

Category: 
Design

Hello everyone,

I have been running several fixbb and flxbb protocols for a while now, but it seems the outcome is not very promising.

So i guess mainly the issue is with disordered structures? Whatever I RosettaDesign i always end up with decoys that have intrensic disrodered states for the majority of the residues in a structure.

this of course affect the folding simulation to determine the success of the design, as well as the crystallisability of the structure.

Post Situation: 

MSDMover error in RECON protocol

Category: 
Design

Hi Everyone,

I'm sorry to open a new topic about the RECON multi-state design. I got the same error when I run Rosetta when I used mpi (I tried two Rosetta versions 2016.08 and 2018.09). In the error message, it said I need to pass the -run:msd_job_dist flag to make it work (I did and it still didn't work).  Here is the error I got:

Post Situation: 

Multi-state design with the error "unable to locate database file"

Category: 
Design

Hi,

I am a new Rosetta user and learning to do the multi-state Ab design by following the RECON protocal. When I run it, I got the error said "unable to locate database file" even though I already listed the database path in .options. Could anyone help me to fix this problem? Here is the error message I got:

Post Situation: 

Segmentation Fault

Category: 
Docking

Hi,

I am trying to use protein-protein docking with unbound ligand protein and, I still get this error(see below ). I would appreciate any suggestion or solution.

Looking forward to hearing from you.

Haresh 

 -------------------------------------------------------------------------

Post Situation: 

Pages

Subscribe to RSS - Unsolved