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On iterations in ddg_monomer

Submitted by Proteinmechanic on Fri, 2022-09-30 21:23
Category: 
Structure prediction

Dear community, 

I am just beginning to explore Rosetta with some mutational analysis. 

Currently exploring ddg_monomer. 

From what I have read so far, ddg_monomer doesn't have parallel support. 

Could I please know if setting 

-ddg::iterations 1

and then repeating the above 49 other times, to make a total of 50 predictions and then choosing the top three stated in the manual would produce similar results as setting 

-ddg::iterations 50

and running only once. 

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Rosetta 3 - General

GeneralizedKIC side chain closure.

Submitted by almeida85 on Mon, 2022-09-19 06:13
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.

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Rosetta 3 - General

academic_address

Submitted by Natalia on Fri, 2022-09-16 12:27
Category: 
ROSIE

Hello! I am a student of Pirogov Medical University and an employee of N.N. Blokhin NMRCO. My thesis work is related to the modeling of protein-protein interaction. Our domain address @ronc.ru 
Please approve an academic address!

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ROSIE - General

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

Submitted by to-qinbin@163.com on Wed, 2022-09-14 06:06
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
 

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Rosetta 3 - General

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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