The problem hasn't been solved
"Submitting Rosetta-Vienna RNP-ddG job failed!
Validation failed as:
Please correct this errors and re-submit!"
Hello,
I am using several applications with mpi (docking, pepspec, simple_cycpep_predict) and I get repeated entries of the same result with different scores.
Hello,
I've been trying to incorporate a noncanonical selenium-containing residue into my protein sequence, however, when running molefile_to_params_polymer.py I keep getting an error saying "unknown element SE." I've tried looking at the code where the error occurs, and it seems there are a series of elif statements that specify some atoms that are allowed. That being said, I swapped selenium out for xenon (not listed in the code) in the sdf file and the function ran to completion. I've attached a screenshot of my SDF.
Hi,
I am using rosetta for modelling the peptide from a pMHC complex. I have been using a template which I thread into the target sequence which I use in a loop modelling protocol.
When modelling I only focus on the peptide without letting any part of the MHC move, but in some cases, I have bad modelling results.
I was wondering if including the residues of the MHC in contact with peptides in the modelling will be a way to improve the results I am getting.
Hi,
I am using rosetta for modelling the peptide from a pMHC complex. I have been using a template which I thread into the target sequence which I use in a loop modelling protocol.
Until now the templates that I used had a high sequence identity with the target, but now I have cases where the identity is 3 out 9 or even less.
My question regarding this is:
Hello,
I am using simple_cycpep_predict in design mode to find derivatives of a peptide for disulfide cyclization. For the -cyclic_peptide:allowed_residues_by_position option I am using the following file:
I encountered this error while trying to login to ROSIE:Your GitHub account does not have verified academic email address! My academic domain ( @kribb.re.kr ) cannot be verified during login to rosie. My institution is public research organization in south Korea
Thank
Hello,
I am using Chemicel-Shift-Rosetta for protein structure determination and I would like to fix a cofactor in my protein. Does anyone have an idea how to do so?
Thanks!
Hello, everyone, I encountered some problems when I was doing Step 19: Actual motif grafting of RIFdocking.
First, I need to turn my scaffolding into a silent files. The command is as follows:
cat scaffolds.list | silentfrompdbsparallel > scaffolds.silent
After the command is run, I got the following error:
