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De Novo backbone generation vs Rosetta Match for enzdes and ligand binding.

Category: 
Enzyme Design

Howdy Yall, 

So I have not been in the Rosetta world for very long, and most of what I have learned I have had to parse from the Rosetta Commons Demos/Documenation and various publications since no one else at my institution does this sort of work. So while I have learned quite a bit, there is some fundamental questions about approach/methodology that I feel blind towards.

Post Situation: 

Problem with 'AddEncounterConstraintMover'

Category: 
Docking

Greetings, I'm trying to reproduce a local protein-protein docking using replica exchange methods published in this paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010124

After I run I receive  the followinf error message:

 

[FILE]: src/protocols/rosetta_scripts/RosettaScriptsParser.cc

[LINE]: 1192

[START_MESSAGE]

Post Situation: 

CONECT information for PDB files by raw sequence

Category: 
PyRosetta

Hello,

I create a pose from sequence and dump it as PDB:

pep_pose = pyrosetta.pose_from_sequence(sequence, res_type='fa_standard', auto_termini=True)
# pep_pose = pyrosetta.Pose()
# pyrosetta.rosetta.core.pose.make_pose_from_sequence(pep_pose, sequence, 'fa_standard', auto_termini=True)
pep_pose.dump_pdb(pdb_file_path)

As I understood, 'pose_from_sequence' creates a peptide structure by sequence, but what I found was that the PDB file misses the whole CONECT information.

Post Situation: 

Simplest rosetta compilation

Category: 
Compilation

I used to compile rosetta with mode=release ~5 yrs ago with no problem.

But now I can't..

With

rosetta_bin_linux_2021.16.61629_bundle

Red Hat Enterprise Linux Workstation release 6.6 (Santiago)
Release:    6.6

I tried

scons.py -j4 bin mode=release

Then, I see

Post Situation: 

rosetta.build_phenix_interface on fedora 36

Category: 
Compilation

This is for those who are interested in building rosetta_phenix_interface on fedora 36 or in general using gcc 12.1.1 20220507.

I had no problem compiling the phenix interface using rosetta.source.release-314 on fedora 36 after two little tweaks:

Post Situation: 

Pepspec error

Category: 
Design

Hello,

I am using pepspec in design mode, working with a peptide bound to a protein pocket. When I run the command (pepspec.linuxgccrelease -database $ROSETTA_DB @spec.args) I get the following error:

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

Post Situation: 

abinitio demo is not progressing - new install

Category: 
Compilation

Hey, I am a relatively new user and my University recently got an academic license and installed Rosetta on our high performance computing for my PhD in de novo design after requesting. I am trying to run the abinitio demo contained within "/rosetta/3.13/gcc-9.3.0+openmpi-4.0.4/rosetta_src_2021.16.61629_bundle/main/demos/public/abinitio" but I am running into a strange error.

Post Situation: 

How do I change the default Compiler for Rosetta?

Category: 
Structure prediction

Hello Rosetta users,

 

I have a few questions with respect to antibody modelling in Rosetta.

 

The current version of Rosetta I'm using is a pre-compiled version 3.13 of Linux.  I always get an error when I perform the first step of Antibody Modeling:  

antibody.static.linuxgccrelease \

    -fasta antibody_chains.fasta

 

I checked and found that the solution to this problem was to install a higher version of GCC.  

Post Situation: 

CONDA_OVERRIDE_GLIBC=2.27

Category: 
PyRosetta

Not a question, but a note of an issue to save anyone getting lost by it

I had a spot of bother installing PyRosetta on a cluster running Ubuntu as PyRosetta was giving:

lib64/libc.so.6: version `GLIBC_2.27' not found

(Dejavu of pytorch, anyone?)
To fix it the system environment CONDA_OVERRIDE_GLIBC=2.27 does the trick:

Post Situation: 

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