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peptide design

Submitted by Miriam Gulman on Wed, 2023-10-25 00:09
Category: 
Design

Hi, 

I have a protien peptide complex and I want to design a peptide that will bind to the protein better the the WT peptide. What tools do you suggest I use? it can also be from

any of the other rosseta platform (or any other). My goal is to find 50 potential peptides and then test them experimentally.

Thanks, 

Miriam

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ROSIE - General

rosetta_cm - ERROR: Assertion `tlen < slen` failed on File: src/core/fragment/util.cc:177

Submitted by ramon-arg on Thu, 2023-07-13 18:41
Category: 
Structure prediction

I'm following this tutorial to run a protein structure prediction: https://new.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

I was able to model one protein sequence successfully following those steps, but trying for different ones I've been getting this same error:

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Rosetta 3 - Applications

fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz

Submitted by yueyuedake on Wed, 2023-07-12 03:36
Category: 
Structure prediction

Hi,

When I run fragment_picker, it gives the message:

ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
ERROR:: Exit from: src/protocols/frag_picker/VallProvider.cc line: 17
 

the detail message as follows:

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Rosetta 3 - Applications

Post-traslational modifications

Submitted by diegoms on Wed, 2023-06-21 01:22
Category: 
Chemically Modified Residues

Hello, everyone

I was trying to study the effect of post-translational modifications on the structure of proteins. For that purpose, I followed two different approaches:

  1. I modified the residue with a variant using pyrosetta.rosetta.core.pose.add_variant_type_to_residue. Then, I replaced the original residue with the modified one using pose.replace_residue().

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PyRosetta - General

Converting all residues to poly-Gly/Ala

Submitted by jtpi6174 on Tue, 2023-05-09 14:14
Category: 
Enzyme Design

Hey, I am pulling my hair out over this. I am trying to convert all residues in a protein to poly-Gly/Ala (for example 1ae1.pdb) but cannot find the Rosetta function to do so. I am replicating a paper where they included code and output, the output appears to be typical Rosetta output (the .pdbs are like 3tzc___1.pdb) which I am assuming were generated with a Rosetta function.

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Rosetta 3 - General

XML validation failing

Submitted by mb0261 on Fri, 2023-04-14 14:53
Category: 
Docking

I am trying to validate a .xml script to be used by rosetta_script application. I copied the .xml file from the paper:  Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein−Ligand Docking. But the valdation fails...

When I run, 

validate_rosetta_script.default.linuxgccrelease -parser:protocol crystdock.xml -parser:script_vars sg=input random=0

 

Here is my XML:

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Rosetta 3 - Applications

Error compiling in old macOS El Capitan 10.11.6

Submitted by dfcoelho on Wed, 2023-03-29 09:59
Category: 
Compilation

Hi all,

I am trying to compile Rosetta-334 week 45, year 2022 in my old friend Mac Mini with macOS 10.11.6 El Capitan.

I am using the standard command line: 

./scons.py bin mode=release -j4

After a few second I've got the following error:

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Rosetta 3 - Build/Install

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