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EMERALD method not working, Rosetta version not available for download

Submitted by seba on Thu, 2023-05-04 08:14
Category: 
Small Molecules

Hi,

I am trying to reproduce the the results from this paper 'Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps', but when I try to run the script from the paper (de3mo) i'm getting the following error:

File: src/utility/options/OptionCollection.cc:1467
Option matching -in:file:override_database_params not found in command line top-level context

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Rosetta 3 - Applications

relax protein with multi-conformer bound ligand

Submitted by xfradera on Thu, 2023-01-12 09:10
Category: 
Small Molecules

I am working with a protein with a bound small molecule (non-covalent). I've managed in creating parameters for the ligand and relaxing the complex following this workflow: https://new.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README

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Rosetta 3 - Applications

Trehalose

Submitted by jpfuenzalidawx on Thu, 2022-09-08 00:49
Category: 
Small Molecules

Hi,  I am having trouble minimizing a protein that contains trehalose. Unfortunately, Rosetta does not like trehalose and always deforms it.  

I have no problems with glucose, that's weird because trehalose is a glucose disaccharide.   I am using the flag -include_sugars and the relaxed structure has unrealistic energies because it forces the formation of non-existing bonds.  The main problem is that rosetta assumes it is ->2)-alpha-D-GlucP

 

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Rosetta 3 - Applications

PDB weird to PDB rosetta friendly

Submitted by jpfuenzalidawx on Fri, 2022-09-02 04:43
Category: 
Small Molecules

Dear all,

 

I want to relax a protein with a ligand in a specific position using the simple "relax.linuxgccrelease" program. However, I found that if the atom names (third column at the PDB) are not as expected, the output "relaxed" PDB shows a weird ligand (it looks more like an insect than a molecule), regardless if the ligand is already parameterized in Rosetta (Sorbitol [SOR] in this case). Once the atom names are fixed, the relaxed structures make sense.

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Rosetta 3 - General

Ligand Docking with ROSETTA

Submitted by sc19 on Thu, 2022-07-14 01:32
Category: 
Docking
Small Molecules

Hi,

I have been trying to perform Ligand Docking with the ROSETTA software. I describe what I have done:

1. First, I have the ligands in sdf/mol2 format one per file. I add hydrogens to these and create the params files with the "molfile_to_params.py" script.

2. Second, I clean the protein (no ligands or cofactors) and add H to the protein.

3. Third, I concatenate the protein with each ligand in a different file for each ligand (the ligand has chain identifier X, the protein A).

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Rosetta 3 - Applications

-ignore_unrecognized_res doesn't work

Submitted by e3lm on Fri, 2022-05-06 14:47
Category: 
Small Molecules

Hi, I'm minimizing structures in a list of PDB's using the -l option. Some structures have different ligands which I'd like to ignore or skip. The -ignore_unrecognized_res doesn't work. Minimize got bumped out trying to fill in missing atoms. Apparently it did not see or understand the flag.

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Rosetta 3 - General

Pose is full atom and mover expects centroid, how do I handle it the best?

Submitted by hlinn on Thu, 2022-01-27 05:55
Category: 
Small Molecules

I'm trying to use pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader for a project of side-chain packing small peptides with a fixed backbone. I've gotten as far as building the Mover: instantiate the mover, giving it rebuild info and the string with selected rotamers.

The problem I run into comes when I try to apply it to the starting pose; I get a warning:

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PyRosetta - General

Problems with waters in CoupledMoves application

Submitted by Corvin on Tue, 2021-11-16 07:16
Category: 
Structure prediction
Docking
Small Molecules

Kind strangers,

I am writing you in a hope that the following problems will be resolved with your help.

I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.

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Rosetta 3 - Applications

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