Hi there!
Hello,
I am designing a macrocycle with simple_cycpep_predict that contains a D-Leu in the N-terminal and an acetylated ASP in the C-terminal. My sequence_file (-cyclic_peptide:sequence_file) is DLE ........ ASP
1) When I run the app it doesn't recognize the D-Leu name:
Hi everyone,
I am trying to design a nanobody using an available antibody. After grafting heavy chains from an antibody to a known nanobody scaffold, and aligning with the antibody-antigen complex structure, I obtain nanobody-antigen compelx structure. I am trying to use Rosetta design to increase its affinity to antigen as well as sample possible new CDR sequences using the options,
Hello,
I am using simple_cycpep_predict in design mode to find derivatives of a peptide for disulfide cyclization. For the -cyclic_peptide:allowed_residues_by_position option I am using the following file:
Hello, everyone, I encountered some problems when I was doing Step 19: Actual motif grafting of RIFdocking.
First, I need to turn my scaffolding into a silent files. The command is as follows:
cat scaffolds.list | silentfrompdbsparallel > scaffolds.silent
After the command is run, I got the following error:
Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. An error occurs when I run the command: Signal 6 (SIGABRT) means that the process was aborted. This usually means an internal Rosetta error caused by (often) bad inputs, (sometimes) developer error, or (rarely) hardware problems.
Has anyone encountered this error with Rosetta? How can I solve this problem? I'd be grateful if you could give me any help.
Hi! I ran into a problem when I was repeating the article "Design of protein binding proteins from target structure alone". The protocol I was followed is cao_2021_protocl_guide.txt. The step I was running is 12th: running a pilot job which is a protein interface design. could anyone help solve this problem?
Hello,
I am using Pepspec to optimize a 10mers peptide sequence to better binding to a membrane protein. In the design, I kept the first residue constant, while mutating the rest by all 20 amino acids. The flags file is the following:
-in:file:s ppk_complex_0001.pdb
-pepspec::pep_chain B
-pepspec::pep_anchor 1
-pepspec::n_append 9
-pepspec::n_peptides 10000
Hi all!
I am trying to generate a file with all the parameters for the monomer of a rigid polymer.
Is there any special way? Because the param file that I obtain is different from, for example, aminoacids.
Thank you in advance.
Hi Rosetta Team!
I am trying to use RosettaScripts to design side-chain conformations to a protein backbone.
Unfortunately, the output score.sc only shows total_score and with all zeros.
