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

Submitted by aanshi on Wed, 2022-11-23 11:13
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!

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Rosetta 3 - Applications

Loop modeling

Submitted by Robertofg on Tue, 2022-11-22 00:34
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

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Rosetta 3 - General

N-Terminal Galactose

Submitted by SebastianBB on Mon, 2022-11-21 08:33
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?

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Rosetta 3 - General

Rosettadock Error

Submitted by jinfeng on Fri, 2022-11-18 20:39
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:

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ROSIE - General

snugdock: constrained backbone

Submitted by mahendra on Mon, 2022-11-14 02:51
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,

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Rosetta 3 - Applications

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

Submitted by JasonIsaac on Sun, 2022-11-13 03:41
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.

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Rosetta 3 - General

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