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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

connecting rna strands together

Submitted by y_atsmonraz on Tue, 2021-11-09 05:42
Category: 
Nucleic Acids

Hi there, could anyone please tell me how I can connect two rna strands together via a known linker  that I don't have a structure for ?

Supposedly: RNA 1 is uaugaaaaua

RNA2 is cggcgaaagccg

and their linker is uuu

making a total of :

uaugaaaauauuucggcgaaagccg

How can i do this via rna_denovo?

 

Thanks in advance for any help!

 

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Rosetta 3 - Applications

PIPER-FlexPepDock protocol file apply_ftresult.py missing

Submitted by diasmarieli on Thu, 2021-11-04 06:33
Category: 
Docking

Hello,

I've been trying to run the PIPER-FlexPepDock pipeline in both ways, following the steps in the documentation page (https://www.rosettacommons.org/docs/latest/application_documentation/docking/flex-pep-dock), and using the scripts in the "tools/peptide docking" folder. But both cases need the script "apply_ftresults.py" which doesn't exist in the source. Where can I get this script or any equivalent?

Thank you in advance.

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Rosetta 3 - General

The energy terms in InterfaceAnalyzer

Submitted by Sunyp_IM on Tue, 2021-11-02 18:43
Category: 
Scoring

Dear All,

There are many energy terms in the output of the InterfaceAnalyzer, but is there any articles or other forms of materials  which explain the basic principals or mathematical formats for calculating these energy terms in detail? And How rosetta codes for them? If I wished to add some energy terms in InterfaceAnalyzer, What is an effective way to learn the coding for this propose? 

I will appreciate any help. With many thanks.

 

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Rosetta 3 - Applications

Error in compilation with rosetta.build_phenix_interface

Submitted by vcalderone on Fri, 2021-10-29 22:35
Category: 
Compilation

I have installed the last version of phenix ( phenix-1.20rc2-4400) and then I have tried to compile the last weekly version of rosetta (rosetta_src_2021.07.61567_bundle) with 'rosetta.build_phenix_interface nproc=8'

The machine is Fedora 34 with gcc -v:

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Rosetta 3 - Build/Install

Error when testing rosetta.run_tests

Submitted by biomics on Thu, 2021-10-28 23:01
Category: 
Compilation

Hello,

I have tried to install Rosetta (version 3.11) for use in Phenix (version 1.19.2) on ubuntu 18.04. No problem with Phenix installation and rosetta.build_phenix_interface nproc=24, but when I run rosetta.run_tests, I got the following. 

==

Generating 2 models on 1 processors...

DEBUG dumping error message
ERROR: Rosetta exited with status 139
stderr output:

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

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Rosetta 3 - Build/Install

building a protein-dna homology model via cm_rosetta

Submitted by y_atsmonraz on Wed, 2021-10-20 23:11
Category: 
Nucleic Acids

Hello everyone, recently I've been trying to make a homology model with a protein chain along with a nucleotide chain within it based on an existing template, but .

post-partial threading Rosetta dislocates the nucleotides nearly 1000 angstrom away from the structure. .

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Rosetta 3 - Applications

Installation of Rosetta on Mac BigSur

Submitted by rashmijain on Tue, 2021-10-12 15:06
Category: 
PyRosetta

Hi, 

 

I have installed pyrosetta and rosetta on my system and when I try to import in my python code it says module not found. I have a BigSur mac computer. Is it because of my system? Can someone help me who has also installed it on bigSur?

Thank you in advance!

Best,

Rashmi

 

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Rosetta 3 - Build/Install

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