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I have recently started using Rosetta and I wanted to generate the 3-mer and 9-mer fragments for Abinitio (without using the Robetta server).
I used the make_fragment.pl files provided under the fragment_tools folder in Rosetta to generate the files (by giving just the fasta file as an input). However, the result that I gathered was not the same, as what is generated by the Robetta server.
Recently I'm stumbling with rosetta RAbD application (version 2020.08.61146) in hope to modify an antibody whose antigen containing a non-canonical,N-term, and PRO-like aa ,namely the pyroglutamic acid in its epitope.
I generated params file according tutorials in :https://new.rosettacommons.org/demos/latest/public/design_with_ncaa/README,with input mol file below.
I would like to assess my designs using the fragment quality metric and biased forward folding. In both cases Rosetta documentation suggests to use the r_frag_quality application. However I cannot find it in my locally compiled versions of rosetta (for example in rosetta_src_2020.08.61146_bundle). Can anybody help?
I'd like to make abinitio structure prediction using rosetta of some small proteins (e.g. 2jof, which length is 20 amino acids).
Such prediction requires fragment files, which can be generated using web Robetta Server or by youself using PSI-BLAST.
However, when i tried to submit a job on Robetta there was an error:
Sequence length must be between 27 and 1000 residues
Similar restriction was described in rosetta manual dedicated fragment-files:
I am trying to run make_fragments.pl but I get this error:
Running sparks for phi, psi, and solvent accessibility predictions
running psiblast for sequence: lig_0.fasta
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix