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I'm using rosetta_src_2020.08.61146_bundle. I'm trying to use the RosettaAntibody3 workflow as documented here, but am running into the following error when I run the following command:
module load rosetta/2020.08 blast/2.10.0+ gcc/9.1.0 antibody.default.linuxgccrelease -ignore_unrecognized_res true -fasta IL6antibody.fasta -out:path:all antibodied
Here is the IL6antibody.fasta file:
I don't know if this is the appropriate place to ask this type of question but I have been reading this paper which describes the FastFloppyTail and Abinitio programs:
Hope everybody is doing well.
I'm just getting used to using Rosetta and would appreciate some pointers with regards to comparative modeling of metalloproteins.
I have a protein (155 amino acids) that binds to Zn. I know exactly which amino acids the zn atoms interacts with and I have 2 homologs for templates with homology in the 65% region. I've been reading this tutorial
I'm trying to use the antibody executable to create a model of an exisiting antibody. I have the CDR sequences that I need to model, so I created a fasta file and tried to run it. However, I get this error:
ERROR: Unxpected length of h1 [length=3], length expected to be: [6, 7, 8, 9, 10, 11, 12, 13]!
I've run into an issue building a model using denovo_density in step 4D of this protocol: https://faculty.washington.edu/dimaio/files/rosetta_density_tutorial_aug18_4.pdf,
The rosetta command that throws the error is:
Hi, I'm trying to group structures into clusters, but I have an error and an empty log file. A few months ago (in February / March) I didn't have a problem with it, although I did it in the same way (I think so). I have no idea where this problem comes from.
Using the AbinitioRelax protocol, I obtained a silent file with 100,000 structures (centroid representations) for a certain amino acid sequence. Now I want to group the structures into clusters and sort by energy. I use the following commands:
I'm new to rosetta design and looking to do ab initio folding for my first metalloprotein design. I saw the documentation (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/metalloprotein-abrelax), looked at the test inputs, and read the original paper. All of these only address His and Cys as ligands. Is there a way to do other ligands such as Glu or Asp?