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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")

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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:

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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.

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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. 

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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 ]

 

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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!

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ROSIE - General

Nanobody design

Submitted by chandana on Tue, 2022-08-09 20:36
Category: 
Design

Hi everyone,

I am trying to design a nanobody using an available antibody. After grafting heavy chains from an antibody to a known nanobody scaffold, and aligning with the antibody-antigen complex structure, I obtain nanobody-antigen compelx structure. I am trying to use Rosetta design to increase its affinity to antigen as well as sample possible new CDR sequences using the options,

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Rosetta 3 - Applications

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