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N-Terminal Galactose

Category: 
Chemically Modified Residues
Non-Canonical Peptides

Hi,

I want to modell the HbA1c (Hb with Galactose bound to the N-Terminal Val) N-Terminal residues.

I can't find a matching paramterset for the Galactose in the database. The to6-*-*-Galp.param is very close except that instead of the O6 atom, the C6 is bound to the N of the Val.

What is the best way to add the right parameters as a new residue type? Copy the to6-*-*-Galp.param files and modify just the atoms bound to the N or start from scratch?

How would the new *.param file look like?

Post Situation: 

Rosettadock Error

Category: 
Docking

Hi,

I tried to dock a ligand protein to a receptor (a dimer) by using the rosettadock websever, but unfortunately it failed. I did not get the docked conformations. My job id is 4910. In the 2.docking.output.0 file, there is the error message:

Post Situation: 

Error in rosetta_scripts.mpi.linuxgccrelease: double free or corruption (!prev): 0x0000000007697a90

Category: 
Design

Hello,

I am running  a xml script with rosetta_scripts (Rosetta 3.14, v2022.11) in my HPC cluster and I am getting the following error:

Post Situation: 

snugdock: constrained backbone

Category: 
Docking

Hi,

I am running snugdock for Antigen-Antibody docking. As I can see from the output pdb files, the loops are moving during docking.  After reading snugdock paper I do see the reason for that.

But in my case, I would like to fix the backbone of both Antigen and Antibody (for loops and nonloop regions). 

I tried to include "-relax:bb_move false" flag, but it seems like it is doing nothing.

does anyone know how to fix the backbone during snugdock docking?

Many Thanks,

Post Situation: 

Where is Sicdock application now? Can I find a substitute?

Category: 
Docking

Greetings,

       I am trying to reproduce the results of paper "Computational design of a homotrimeric metalloprotein with a trisbipyridyl core". I found that this research used an application named sicdock.ompstatic.linuxgccrelease to carry out docking calculations. But I can't find it in newly released Rosetta version. My foucs on Macbook can't find any application related to sicdock but only some options file and .cc file.

Post Situation: 

Error with sequence_tolerance.R processing the checkpoint files, *.ga.entities and *.ga.generations.

Category: 
Scoring

Hello,

the output files, *.ga.entities and *.ga.generations, were produced by sequence_tolerance application. 

When I tried to use sequence_tolerance.R processing the output files, I got the following error:

> source("/usr/local/rosetta_src_2021.16.61629_bundle/main/tools/analysis/apps/sequence_tolerance.R")

> process_seqtol("./2I0L_A_C_V2006_0001.ga.entities")

Post Situation: 

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