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Ligand docking score.sc file containing more structures than produced

Submitted by Delfosse57 on Sat, 2022-07-16 10:44
Category: 
Docking

Hello,

I was performing various ligand docking procedures using Rosie and when I was analyzing the data I noticed that some decoys had multiple entries in the score file with different scores but the same decoy model name. Is this normal and if so how can I interpret it?

For example one of my procedures created 200 docking models but the score file had 204 entries, 4 of which referenced already referenced models.

Thank you!

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ROSIE - General

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

Submitted by csvajda on Thu, 2022-06-30 09:55
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.

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Rosetta 3 - General

Problem with 'AddEncounterConstraintMover'

Submitted by mb0261 on Tue, 2022-06-28 10:00
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]

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Rosetta 3 - General

CONECT information for PDB files by raw sequence

Submitted by Fata on Wed, 2022-06-22 01:47
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.

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PyRosetta - Scripts

Pepspec error

Submitted by almeida85 on Mon, 2022-05-02 04:07
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.

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Rosetta 3 - Applications

abinitio demo is not progressing - new install

Submitted by jtpi6174 on Thu, 2022-03-24 03:49
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.

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Rosetta 3 - General

How do I change the default Compiler for Rosetta？

Submitted by pagumaaaaa on Wed, 2022-03-16 00:23
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.  

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Rosetta 3 - Applications

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