You are here

Home

Unsolved

The problem hasn't been solved

Multiple Relax runnings

Submitted by mb0261 on Sat, 2022-08-27 05:42
Category: 
Docking

Greetings everyone,

I actually have a general question, nothing specific to a rosetta protocol. But whenever I tried running multiple calculations on a HPC that uses the same application at the same time - i.e. run 3 relax protocol for protein-protein docking, the calculations simply just stop without giving me any  ROSETTA_CRASH.log, or even going through all models. What might  be the reason? What can I do ?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Using specific rotamers

Submitted by sahn97 on Fri, 2022-08-26 13:45
Category: 
Docking

We're trying to run a docking study between two proteins, with the protein to be docked has a few residues with some rotamers. We want to fix these rotamers, but no matter what we try, Rosetta seems to change the rotamers between the poses. Is there a way for the rotamers to be completely fixed, so that we are docking the same version of the protein in each pose?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

machine designation 'ppc64le' is unsupported

Submitted by tarsis on Tue, 2022-08-23 06:22
Category: 
Compilation

Hi,

I'm trying to compile rosetta 2021.16.61629 at cineca but it seems that ppc64le is unsupported. Any help on what to do to fix this would be much appreciated. Please see below:

scons bin mode=release extras=mpi extras=hdf5 

Traceback (most recent call last):

 File "/m100_work/icei_Marfor2_0/UBQ/rosetta_bin_linux_2021.16.61629_bundle/main/source/SConstruct", line 183, in main

    build = SConscript("tools/build/setup.py")

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

Macrocycle from a C-terminal amidated peptide

Submitted by almeida85 on Thu, 2022-08-18 07:53
Category: 
Non-Canonical Peptides

Hello,

I want to generate a macrocycle of a 10 residues peptide, that has an amidated C-terminal residue.

For this, I am playing with simple_cycpep_predict with the -cyclic_peptide:cyclization_type sidechain_isopeptide flag to get crosslinked sidechains between positions 5 and 10, i.e, LYS5 ... ASP10 (ASP10 is amidated). I have a lineal peptide pdb of the same sequence that I would use as native). My command line and flags are:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

academic email

Submitted by rhn on Wed, 2022-08-17 12:44
Category: 
ROSIE

I encountered this error while trying to login to ROSIE:Your GitHub account does not have verified academic email address! My academic domain (@stowers.org) cannot be verified during login to rosie. My institution (Stowers Institute for Medical Research) is a nonprofit and academic biomedical research institution in the US.

Post Situation: 
Unsolved
Forums: 
ROSIE - General

GeneralizedKIC disulfide closure

Submitted by Ken on Tue, 2022-08-16 13:32
Category: 
Loop Modeling

Hi all,

I have been banging my head against the wall on this for a while now, and I think it's time to get help.  Here is my problem.  I'm trying to understand how to close loops in a toy example via different residues (head to tail, side-chain/side-chain, disulfide, etc) with GenKIC and I cannot for the life of me understand what the error message is trying to tell me. 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Docking HeparinSulfate to proteins using GlycanDock

Submitted by GebauerJ on Tue, 2022-08-16 07:44
Category: 
Docking

Hi all,

back in the days I have use Rosetta for protein de novo prediction, but never went really deep into it.

I now wanted to use the GlycanDock application to dock an heparin molecule to a protein. However, GlycanDock does end during preparation with this error message: 

ERROR: Cannot compute center of mass of zero residues!
ERROR:: Exit from: src/core/pose/util.cc line: 1408
protocols.jd2.JobDistributor: [ ERROR ]

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Error Fasta file

Submitted by gabrielab on Mon, 2022-08-15 00:41
Category: 
Structure prediction

Hello,

I am trying to predict antibody structure but I keep getting an error message when choosing the fasta file containing the heavy and light chain. I am using the ">heavy" and ">light" marker in the fasta file but it doesn't seem to recognise the sequences. I am not sure what I am doing wrong. I am attaching an image of the error message for reference. 

Thanks for your help!

Post Situation: 
Unsolved
Forums: 
ROSIE - General

Unrecognized D-Leu name / C-terminal ACE

Submitted by almeida85 on Thu, 2022-08-11 07:43
Category: 
Design

Hello,

I am designing a macrocycle with simple_cycpep_predict that contains a D-Leu in the N-terminal and an acetylated ASP in the C-terminal. My sequence_file (-cyclic_peptide:sequence_file) is DLE ........ ASP

1) When I run the app it doesn't recognize the D-Leu name:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Unsolved