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I am trying to design the interface of a peptide docked on a protein. For that, I have written a design XML considering only peptide residues to be designed. I use a docking tree mover that should define 1 jump in the sequence, but when I run the script I always get the same error:
[ ERROR ] UtilityExitException
ERROR: Cannot compute center of mass of zero residues!
Greetings Rosetta developers,
I am trying to use BackrunDD via rosetta_scripts (Rosetta ver 3.9). But I could not help but notice the difference between the available attributes for BackrubDD when I run ' rosetta_scripts -info BackrubDD' and those documented in the following link:
I used backrub server for flexible modeling and the results of my run sent to my email address. but unfortunately I can not download my results and I got an error. I tried to download my results in several days but I got an error again. what is the problem and how can I solve it? thanks
I have a protein-peptide(15 a.a) system with alreaddy a good guess for the binding mode of the peptide. Now I want to move slightly the peptide to a more reactive conformation and design mutants in this reactive conformation.
The “enzdes” application with a constraint file would do exactly what I need but I think it was created for “protein-small ligand” systems and I cannot use it with a multiple residues ligand like my peptide.
I'm running Rosetta single state design (though I imagine my question applies to MSD as well), which works great on a single core or my local machine. I'm using rosetta_scripts.mpi.linuxgccrelease as my package. It is compiled by my HPC administrator to function with the cluster.
I my attempt to get a working RosettaDesign protocol, I have come across the RemodelMover() class.
From the Rosetta C++ documentation, the RemodelMover should take a blueprint file in order to specify which residues to remodel. but the RemodelMover() class in PyRosetta has no method to input a blueprint file nor a resfile.
on its own the RemodelMover works without any errors, but would remodel the entire structure.
Sorry to trouble again.
I understand that the multistate design protocol outputs structures where the chains A and B will become AA, AB and BB.
However, I get the output of chains A and B even in the output files AA and BB.
May I find out how I could produce the output files AA and BB homodimers?
Is this something to do with my corr file?
I'm trying to run python /home/labusr/rosetta/main/source/scripts/python/public/molfile_to_params.py --keep-names --clobber --extra_torsion_output --centroid gtp.mol2 -p GTP -n GTP, on a gtp.pdb that has been reduced using phenix.reduce and converted to mol2 using openbabel. Below is the error I get.