You are here

Home

Unsolved

The problem hasn't been solved

Error during docking with proteins containing norleucine

Submitted by aaj on Mon, 2016-04-25 15:04
Category: 
Docking

Hi all The docking of proteins containing norleucine fails with the following error.

can not find a residue type that matches the residue NLU at position 181 can not find a residue type that matches the residue NLU at position 181

ERROR: core::util::switch_to_residue_type_set fails

Is the error related to not being able to find a centroid l-ncaa params file for norleucine?

Would copying centroid MET.params into NLU.params and indicating its location in residue_types.txt work?

Thanks

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

PyRosetta init() error (Linux)

Submitted by FRiemer on Mon, 2016-04-25 01:21
Category: 
PyRosetta

Dear all,

I've been trying (and failing) to build PyRosetta (monolith release 95) for a couple of days now.

I'm running Kubuntu 15.10 64bit.

I've tried running PyRosetta with Python 2.6, 2.6.6 and python 2.7 (ipython & regular).

I never get complaints for from rosetta import * or import rosetta, but when I try to init() I get

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

Problem in refinement job in Docking2

Submitted by aninditaseal on Fri, 2016-04-22 07:12
Category: 
Docking

Hi,

I have recently used the Docking2 program for refining my docked models (job IDs 22582 and 22583). The first has failed due to some problem in the prepacking stage while for the second one the job was finished. For the first one it appears that there was some error in the input file.  The latter although the job has finished it is showing a different error ' 

Post Situation: 
Unsolved
Forums: 
ROSIE - General

Multiprocessor Execution

Submitted by starone on Tue, 2016-04-19 20:06
Category: 
Structure prediction

Hello,

My apologies in advance if this has already been addressed, but I haven't found the answer elsewhere.

I have a powerful workstation with dual Xeons with 16 cores each. dual booting Windows 7 and Ubuntu Linux.  Running on the Windows partition I have used two commercial solutions as well as allowing Rosetta@Home to utilize the system a few hours each night.  Modeling done on all three solutions pegs all 32 processing cores at 100% and the completion times on high quality homology modeling is very low (around 10 hours).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Submitting job to local cluster

Submitted by tusharranjanmoharana on Fri, 2016-04-15 01:38
Category: 
Design

Hi All,

I have installed rosetta on our institute cluster with mpi support (extras=mpi). I want to run rosetta script on the cluster (favor_native_residue.xml). Can anyone kindly let me know how to do it. Attached is a script i used to submit gromacs job in the same cluster (originally it was gromacs_job.sh but I changed it to gromacs_job.txt to attach here) and my favor_native_residue.xml (changed to favor_native_residue.txt for attachment). 

 

Thanks a lot.

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Files for Spatial Constraints

Submitted by Derek on Tue, 2016-04-12 01:00
Category: 
Structure prediction
Enzyme Design
Constraints

Hi guys,

I am trying to locate the files to generate spatial constraints from homologous template structures for comparative modelling as given in the Thompson and Baker paper from 2011. I can't find them anywhere in the ROSETTA directories. Are they available anywhere?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Finding lowest energy structure among generated structures

Submitted by Marius1987 on Sun, 2016-04-10 11:38
Category: 
Structure prediction

Hi Rosetta community,

After finally getting the CS-HM-Rosetta run to successfully generate structures, now I'm at the point where I want to select the lowest energy structure among generated structures which suppose to be the closest to the native structure. But in this website:

https://www.rosettacommons.org/demos/latest/public/clustering/README

there're no instructions on plotting.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Pages

Subscribe to RSS - Unsolved