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Unit Tests failing for Rosetta installed with mpi on Ubuntu 16.04

Submitted by abhi_pe_acharya on Mon, 2016-06-13 22:11
Category: 
Compilation

Dear Users,

I have been trying to install and run Rosetta 2016.15 weekly build (with MPI) on a  core i7 system on Ubuntu 16.04. For installation, I used the following command

> python ./scons.py mode=release extras=mpi bin

and compiled the test scripts using:

> python ./scons.py mode=release extras=mpi cat=test

The system already has openmpi-1.10.2. The installation was without any errors. However, when I ran the unit tests, I got numerous errors with a 27% pass statistic.

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Rosetta 3 - Build/Install

Rosetta: Clustering

Submitted by sskim on Sat, 2016-06-11 14:44
Category: 
Compilation

Hi,

I have used rosetta protein-protein docking to generate 1000 models, and was hoping to use rosetta clustering to analyze the result. 

I have read that rosetta clustering superimposes models for rmsd calculation by default, and I was hoping to find a way to change this default mode for my models.

Is there a way to turn this default mode off? 

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Rosetta 3 - General

How to set up external C++ folding server

Submitted by seanle24245 on Sat, 2016-06-11 10:54
Category: 
Structure prediction

For many of the  Rosetta applications, I am required to connect to an external server to process my requests and handle the modeling and structure predictions.  How exactly am I  supposed to do this?  Is there a detailed tutorial on how to do this?  Or is it because I did not install PyRosetta correctly?  I am doing comparatve modeling/structure prediction.

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PyRosetta - General

Lammps or RosettaSurface

Submitted by StevPChem on Fri, 2016-06-10 10:13
Category: 
Docking

Hello

I hope I placed this question in the proper place. If not please let me know.

I am attempting to computationally dock peptides/proteins to metal oxides etc..What is the most approbriate code to use RossettaSurface or Lammps? At the moment, I have installed PyRosetta and Lammps. Since there is a learning curve using these codes, I would like to select the best one to meet my needs. With LAMMPS, I believe there is versatility (i.e. alter atom types etc..); but I don't know about RosettaSurface..

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Rosetta 3 - Applications

New parametrization problems

Submitted by DmitriiN on Wed, 2016-06-08 05:09
Category: 
Design

Hello all!

I started working with my non-canonical residue REL and found out that it doesn't bond to other residues.

Shall I write some other atoms in the end of mol file?

I am afraid only visualization can help here so I attach the mol file.

Also I attach the created with this mol file params file and one molecule with REL residue.

Thank you in advance,

Dmitrii

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Rosetta 3 - General

Parametrisation problems

Submitted by DmitriiN on Tue, 2016-05-31 09:37
Category: 
Design

Hello everyone!

I have a residue in my protein, that is non-canonical and that I named REL.

After all the steps from https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README with the only difference in using molfile_to_params.py instead of molfile_to_params_polymer.py, because the second doesn't work in my rosetta suite.

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Rosetta 3 - General

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