The problem hasn't been solved
Hello everyone,
I have a protein and I am only interested in modeling two parts of it, constraining the rest of the protein to the structure that we already know. I am new to Rosetta and would like to know what the best approach to this would be.
Here's the source code of mutation_script.xml, part of the demo calculate_protein_protein_ddg included in Rosetta (see https://www.rosettacommons.org/demos/latest/public/calculate_protein_protein_ddg/README). I deleted the comments to make it shorter:
I want to predict the structure of an 85 residue protein, but every time I run abinitio the program stops with no errors or structure output. The protein has a known structure, and I've run abinitio on it successfully. When I remove the .pdb file the output below is all I get. Any suggestions would be greatly appreciated.
My input:
Hi all,
this is the first time I use dock2. I'm trying to submit a docking job. The pdb file is uploaded and displayed, but when I try to submit it a window opens saying "Submitting Docking job..." and nothing ever happens. Any suggestion?
Thank you so much
manu
Hello,
I am trying to create docking poses using D110_DNA_interface.py. For my application I do not need extremely accurate poses (RMSD<0.5) to be created, is there anyway to limit the number of cycles the scripts runs through to create a pose? Ideally, I want to create poses in the range of RMSD between 1-20 angstroms.
I tried using the "Custom docking" commands in the same sample script to change the number of cycles but get the following error:
AttributeError: 'DockMCMCycle' object has no attribute 'get'.
Hi Rosetta Users,
I just started trying the Rossetta symm refinement by using the default settings. However, I ran into the following error messages,
[ERROR] Exception caught by JobDistributor for job chain_B_symm_0001
Hello
My attempts to submit a job in peptiderive server become fail. I cant submit any job in peptiderive server but I am getting no input error job in this server.
Please help me to solve this problem and submit my job in peptiderive.
Thank you
Fatemeh
Hi all,
I've recently started to use the Rosetta suite for some basic modeling of an orphan GPCR. Our research group has discovered several compounds that interact with the membrane protein, either directly or indirectly. To see if any of these compounds could act as ligand, I turend to the ligand-dockng protocol. I went through the tutorial (with some issues) however the results were succesful. Now that I am trying to do it with my orphan GPCR, i've run into some issues:
I have looked at both documentation and this forum, and found no clear answers. I would appreciate it if someone could help.
I have compiled the mpi version to run my "ab initio" structure predictions on multiple cores. I am not sure if I have to change my flags (such as -jran and -constant_seed etc) and my program stalls at protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1
I use mpirun -np 4 path/to/AbinitioRelax.mpi.linuxgccrelease @flag
Thanks, any help appreciated.
-A