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GeneralizedKIC side chain closure.

Category: 
Design

Hi all,

I want to generate cyclic peptides in a binding site employing the anchor design approach similar to https://www.nature.com/articles/s41467-021-23609-8 and  https://www.pnas.org/doi/suppl/10.1073/pnas.2012800118. I need to do the closure by amidation between two side chains (K/E) or side chain/C-terminal.

Post Situation: 

core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP

Category: 
Compilation

core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_DHD
core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP
 

Post Situation: 

Multiple antibody jobs failed

Category: 
ROSIE

 Hello,

I have submitted multiple antibody jobs to the ROSIE-2 server and quite a few of them (Antibody Grafting jobs №3041, №3056, №3067, №3080, №3133, №3144) failed with the following error after already producing some of the 10 relaxed output structures:

[FILE]: src/core/conformation/Conformation.hh
[LINE]: 513
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

 

Post Situation: 

clean_pdb_keep_ligand.py IndexError

Category: 
Compilation

(base) ubun@ubun-System-Product-Name:~/relax/test$ python $ROSETTA/main/source/src/apps/public/relax_w_allatom_cst/clean_pdb_keep_ligand.py 01-MD-086DS.pdb -ignorechain
Traceback (most recent call last):
  File "/home/ubun/rosetta/main/source/src/apps/public/relax_w_allatom_cst/clean_pdb_keep_ligand.py", line 135, in <module>
    if (chainid == line[21] or ignorechain):
IndexError: string index out of range
 

The 01-MD-086DS.pdb file contains a substrate and a cofactor.

Post Situation: 

Residue outside res_map range

Category: 
Constraints

Hi, I am using Rosetta to relax a enzyme with a substrate and a cofactor. The "flags2" was from rosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs

The params file for substrate (DHD.params) and cofactor (NAP) were also used.

But errors!! How to solve this problem?

"flag2"  was scucessfull for the "1A99_1A99.pdb" inrosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs

 

Post Situation: 

Prepacking a macrocycle for docking / preserving cyclization

Category: 
Docking

Dear all,

I have a macrocycle peptide obtained with simple_cycpep_predict, cycled between a Lys (Dap, Dab, and Orn too) side chain and the C-terminal carboxyl. I want to dock this peptide in a binding site with FlexPepDock. During the prepacking step, the bond between the Lys_NZ and the C atom that make the cyclization is lost and a carboxyl is restituted in the C-terminal.

Post Situation: 

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