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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

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Thank you!

Post Situation: 

Help to understand docking results

Category: 
Docking

Dear colleagues, everything's ok?

I have done a docking experiments between enzyme and inhibitor.

I did global docking on cluspro web serve, following did a local and refine docking procedure.

Wight parameters, I should look to compare the docking results with my kinetics data

total score X rms; I_sc X Irms or something else?

I ask for help because some results appear so artificial.

Thanks any way

Ricardo

 

Post Situation: 

RosettaDock output

Category: 
Docking

Hi, now Iam havin gsome trouble about the RosettaDock app.

Few months ago when I proceeded the docking app, I got about 1,000 model resuts as output.

Now I get only 1 model output even though I used same input model and protocol.

Anyone can help me or having same problem with me?

Thank you!

Post Situation: 

Score.sc file showing total score 0 for all protein structures created

Category: 
Scoring

Hello, I am trying to use Rosetta to design the interface of my protein and would like to rank the predicted structures based on their scores however, after running the job, all the files show 0 for the total score. Could anyone take a look at my xml script and flags file (in the pdf file) to see if I'm missing something or how else to fix this issue? Thanks in advance!

Post Situation: 

Loop modeling

Category: 
Loop Modeling

Hello, 

I have a basic question about loop modelling. Can I use the edges as cutpoint or they should be excluded?

For instance, if my loop goes from residues 100 to 109, can residue 100 to be a cutpoint?

Thank you in advance,

Roberto

Post Situation: 

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: 

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