You are here

Home

Unsolved

The problem hasn't been solved

Relevant number of cycles of loop closure required

Submitted by vasavi on Mon, 2018-06-11 02:55
Category: 
Structure prediction
Design
Loop Modeling

Dear All,

I have been working on the Domain insertion module of Rosetta. I need to know what are the relevant number of cycles of loop closure I require to enter for larger domain sets. The domain Im inserting is around 175 aa long. I am having trouble launching the same using MPI in parallel, hence the single processor is taking days for the output. Wondered if anyone who has worked on it could suggest a feasible number for AnchoredPDBcretator and also for AnchoredDesign.

Vasavi.

Post Situation: 
Unsolved
Forums: 
PyRosetta - Applications

installation / python versions

Submitted by rta on Thu, 2018-06-07 00:43
Category: 
PyRosetta

Hi,

I would like to install PyRosetta4 for python 3.6 on Ubuntu 16.04 64bit. For this I installed python3.6, as deafault python version was 2.7. According the installation instruction I have to use smth like

cd setup && sudo python setup.py install

Will it call python 2.7? should I expect any errors? How should I install PyRosetta properly?

Thanks!

 

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

which make_fragments.pl

Submitted by renedominik on Mon, 2018-06-04 08:58
Category: 
Fragment Generation

There are two different versions of make_fragments.pl, several copies under demos/ (all similar except pathes) and one under tools/fragment_tools/.

Latter seems to be more recent, as it refers to the more recent vall.jul19.2011 (which is also included in this release).

But the flexpepdock tutorial points to the version in demos/

Which to use?  (Sorry, if that is a very silly question)

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

ubuntu 16.04 install

Submitted by frankfurter1 on Mon, 2018-06-04 08:55
Category: 
Compilation

Do I assume correctly in a 8 core hyperthreaded machine openmpi runs will be faster than normal static compilations? Has anyone managed to compile  the openmpi version on ubuntu 16.04?   I did have to edit the tools/build/options.settings and add 5.4 otherwise scons wont run.  I assume that the compiler is too new for this? Any work around? Thanks

PS:My tools/build/site.settings is empty

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

How to use MPI with PyRosetta?

Submitted by sn on Fri, 2018-06-01 15:44
Category: 
PyRosetta

Hi,

I am trying to parallelize a protocol using MPI in PyRosetta. I see that PyRosetta does provide interfaces for MPI based job distributors. But, I also saw a documentation stating that PyRosetta doesn't support MPI (https://www.rosettacommons.org/docs/latest/build_documentation/TACC) and recommends using MPI framework provided by Python using mpi4py library. 

Is MPI supported within PyRosetta? How does one typically parallelize PyRosetta protocols?

Post Situation: 
Unsolved
Forums: 
PyRosetta - Applications

"caught exception" for PDB with membrane "DUM" residues

Submitted by nitroamos on Wed, 2018-05-30 08:35
Category: 
Scoring
Membrane
Non-Canonical Peptides

If I run this command:

residue_energy_breakdown.static.linuxgccrelease -in:file:s hasDUMresidues.pdb -out:file:silent energy_breakdown.out -ignore_unrecognized_res true

on the attached pdb, I get this error:

caught exception 

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Dunbrack library takes a very long time to load with custom build

Submitted by sn on Thu, 2018-05-24 16:19
Category: 
PyRosetta

Hi,

I built PyRosetta from scratch with the latest release of Rosetta (2018.19).

Below are the cofigurations of my system:

OS details: CentOS Linux 6.7 64 bit cluster 

Python version 3.6 64 bit

I was successfully able to build the PyRosetta source. However, when I try to run a custom protocol, the Dunbrack library takes a very long time to load. Below is the output after the library loads:

**Dunbrack 2010 library took 618.78 seconds to load from ASCII**

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

solution of the length of peptide candidates is larger than substrate with FlexPepDock and Flexpepbind

Submitted by ziqi1234 on Thu, 2018-05-24 02:18
Category: 
Docking

Hi all,

I'm trying to dock some peptide candidates to a pocket. The pocket of template complex has a 6 aa length peptide , XXXpSXXX. But my peptide candidates I would like to dock is 7 aa length, XXXXXSXX. As you see, the phosphorylation site between substrate and docking peptide don't match on the same position.

My question is

1. Will it be a matter of the enenry score (specially I_sc, pep_sc, etc) if the peptide I would like to dock is longer than the template? if yes, what's the best solution for this case?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages