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Unrecognized D-Leu name / C-terminal ACE

Submitted by almeida85 on Thu, 2022-08-11 07:43
Category: 
Design

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:

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Rosetta 3 - General

Nanobody design

Submitted by chandana on Tue, 2022-08-09 20:36
Category: 
Design

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,

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Rosetta 3 - Applications

simple_cycpep_predict - Design mode - The base name "ARG" was added more than once

Submitted by almeida85 on Thu, 2022-08-04 02:57
Category: 
Design

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:

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Rosetta 3 - Applications

RIFdocking：Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/

Submitted by sia on Tue, 2022-08-02 20:06
Category: 
Design

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:

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Rosetta 3 - Applications

errors about RIFdocking

Submitted by sia on Sun, 2022-07-24 20:45
Category: 
Design

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.

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Rosetta 3 - Applications

protein binder interface design error

Submitted by guowuchen on Thu, 2022-06-23 04:43
Category: 
Design

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?

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Rosetta 3 - General

Pepspec - sequence sampling

Submitted by almeida85 on Thu, 2022-06-23 04:05
Category: 
Design

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

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Rosetta 3 - Applications

Generate template parameter file for a polymer

Submitted by anarob on Fri, 2022-06-10 11:05
Category: 
Design

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.

 

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Rosetta 3 - General

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