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Multiple antibody jobs failed

Submitted by larae on Mon, 2022-09-12 09:54
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.

 

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ROSIE - General

clean_pdb_keep_ligand.py IndexError

Submitted by to-qinbin@163.com on Sat, 2022-09-10 04:04
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.

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Rosetta 3 - General

Residue outside res_map range

Submitted by to-qinbin@163.com on Sat, 2022-09-10 01:56
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

 

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Rosetta 3 - General

Prepacking a macrocycle for docking / preserving cyclization

Submitted by almeida85 on Thu, 2022-09-08 06:54
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.

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Rosetta 3 - Applications

Trehalose

Submitted by jpfuenzalidawx on Thu, 2022-09-08 00:49
Category: 
Small Molecules

Hi,  I am having trouble minimizing a protein that contains trehalose. Unfortunately, Rosetta does not like trehalose and always deforms it.  

I have no problems with glucose, that's weird because trehalose is a glucose disaccharide.   I am using the flag -include_sugars and the relaxed structure has unrealistic energies because it forces the formation of non-existing bonds.  The main problem is that rosetta assumes it is ->2)-alpha-D-GlucP

 

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Rosetta 3 - Applications

Proper indexing of grafted residues by CCDEndsGraftMover

Submitted by cttm4a1 on Wed, 2022-09-07 23:41
Category: 
Design

I found that the grafted residues by CCDEndsGraftMover do not have proper indexing. They have no chain ID, and all residue numbers are 0. If the XML option copy_pdbinfo was set to 1, the grafted residues just shared the same chain ID and residue number as the original segment. I am wondering if there are any movers that do the following tasks.

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Rosetta 3 - General

Sequence symmetry during FastDesign for repeat protein design

Submitted by cttm4a1 on Tue, 2022-09-06 21:02
Category: 
Design

I want to design a repeat protein that self-assembles into a designed structure. As a result, I want each repeat to acquire the same sequence after the FastDesign mover. Is it possible that during FastDesign mover, all repeats are mutated the same way? Is there any Taskoperation (or mover) I can call to set up such a constraint?

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Rosetta 3 - General

PDB weird to PDB rosetta friendly

Submitted by jpfuenzalidawx on Fri, 2022-09-02 04:43
Category: 
Small Molecules

Dear all,

 

I want to relax a protein with a ligand in a specific position using the simple "relax.linuxgccrelease" program. However, I found that if the atom names (third column at the PDB) are not as expected, the output "relaxed" PDB shows a weird ligand (it looks more like an insect than a molecule), regardless if the ligand is already parameterized in Rosetta (Sorbitol [SOR] in this case). Once the atom names are fixed, the relaxed structures make sense.

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Rosetta 3 - General

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