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Ligand being read as part of protein structure

Submitted by MarkusAurelius on Thu, 2021-04-01 11:00
Category: 
Docking

Hi,

I'm attemping a docking run with a protein that acts on an amino acid substrate. (tyrosine) Whenever I initiate the run it gives me the warning:

[ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 W TYS TYR:CtermProteinFull:NtermProteinFull:sulfated

core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CA .

And then the error: 

[ ERROR ]: Caught exception:

File: src/core/pose/chains_util.cc:463

 chain_id W does not exist

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Rosetta 3 - General

Thread target sequence

Submitted by duz on Thu, 2021-04-01 10:09
Category: 
Structure prediction

Hi folks,

when I do threading target sequence, and run the following command:

> $ROSETTA3/bin/partial_thread.default.linuxgccrelease -in:file:fasta 2_threading/1u19.fasta -in:file:alignment 1u19_2rh1.grishin -in:file:template_pdb 2rh1.pdb

I got the following result:

-bash: /bin/partial_thread.default.linuxgccrelease: No such file or directory

do I miss something?

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Rosetta 3 - Applications

params file for beta-amino acids

Submitted by phonez on Mon, 2021-03-29 18:30
Category: 
Non-Canonical Peptides

Hi all,

I've been trying to insert a beta-amino acid into peptide, let's say, beta-homo-leucine. It seems that a params file for beta-hLeu is needed. Unforutnately, there is no params file for beta-hLeu in database in Rosetta, and molfile_to_params.py only works for alpha-amino acid. I've also visited https://rosie.rosettacommons.org/documentation/beta_peptide_design, but did't find helpful solution. So my question is:

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Rosetta 3 - General

Protein Ensemble RosettaLigand Docking

Submitted by sam_dc on Fri, 2021-03-26 10:18
Category: 
Docking

Dear Rosetta Users, 

I have an ensemble of protein conformations obtained by means of MD (Molecular Dynamics) simulation.
I would like to know if a recent protocol is available to dock one ligand to this protein ensemble using RosettaLigand.

 

Thanks in advance.
 

Samuele

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Rosetta 3 - Applications

Can rosetta generate a centroid model based on the rna sequence?

Submitted by yels on Fri, 2021-03-26 04:06
Category: 
Structure prediction

For RNA, what kind of model can be defined as a centroid model?

Does rosetta have a function to generate a centroid model for RNA? For proteins, pose_from_sequence(sequence, 'centroid' ) can be used to generate a centroid model from the sequence. Is there a similar function for RNA?

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Rosetta 3 - Applications

Protocol for adding/mutating non-canonical AA

Submitted by joeri on Thu, 2021-03-25 08:14
Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

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PyRosetta - General

Protocol for adding/mutating non-canonical AA

Submitted by joeri on Thu, 2021-03-25 08:14
Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

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PyRosetta - General

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