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external/dbio/sqlite3/sqlite3.c: Errors

Submitted by janwp on Sat, 2014-09-20 03:27
Category: 
Compilation

Dear all, I keep having problems compiling Rosetta 3.5 on our university cluster. First, I edited site.settings so scons finds mpicc and mpicxx

import os

settings = {

"site" : {

"prepends" : {

"program_path" : os.environ["PATH"].split(":"),

"include_path" : os.environ["INCLUDE"].split(":"),

"library_path" : os.environ["LD_LIBRARY_PATH"].split(":"),

},

"appends" : {

},

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Rosetta 3 - Build/Install

Install rosetta_2014.30.57114_bundle on ubuntu-14.04.1-desktop-amd64

Submitted by lanselibai on Wed, 2014-09-03 07:55
Category: 
Compilation

Dear Sir or Madam,
I want to install rosetta_2014.30.57114_bundle on my Win 7 PC. After installing VMware Player and ubuntu-14.04.1-desktop-amd64, I tried to follow instructions on

https://www.rosettacommons.org/docs/latest/Build-Documentation.html#Comp...

After "Change directory to main/source" and "./scons.py -j1 bin", I was told:

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Rosetta 3 - Build/Install

Parse error while reading in XML file in ROSETTA Scripts

Submitted by rweisse on Fri, 2014-08-29 03:24
Category: 
Design

Hello everybody,

I wanted to run a ROSETTA Scripts script to design a portion of a protein interface. But I struggle with an unexpected error, which appears to occur during reading in the XML protocol. I started the application with the following command line:

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Rosetta 3 - Applications

FlexPepDock Concatenation

Submitted by cam11 on Mon, 2014-08-11 07:39
Category: 
Docking

Hello,

Thanks in advance for all those who help out with this issue. Using the FlexPepDock application, I have generated multiple decoys.silent files (binary) during docking. Multiple decoys.silent files were generated as I used a small cluster of 20 processors where each processor generated its own decoys_X.silent file. Now that I have successfully performed these docks, I would like to concatenate all of the decoys.silent files into a single decoys.silent file for analysis. Is it possible to simply use the method below...

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Rosetta 3 - Applications

Nonstandard residue parameters fail

Submitted by lah435 on Wed, 2014-08-06 17:53
Category: 
Chemically Modified Residues

I'm made parameters for a carboxylated lysine residue as well as parameters for a fluorinated phenylalanine. Both sets of parameters work fine in Rosetta. But PyRosetta throws the following errors when I try to use them or when I add the parameters to the database (whether I use them or not).

>>> res_set = generate_nonstandard_residue_set(['KCX.params','PFF.params'])
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 8524 residue types

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PyRosetta - General

rosetta_2014.22.56873: Unknown argument: '-finline-limit=20000'

Submitted by franfdez on Wed, 2014-07-30 02:17
Category: 
Compilation

I am trying to install rosetta_2014.22.56873 on an iMac [OSX 10.8.5; Darwin Ms-iMac.local 12.5.0 Darwin Kernel Version 12.5.0: Sun Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64 x86_64] but the compilation failed with the following message:

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Rosetta 3 - Build/Install

Pre-packing a model for SWA loop building

Submitted by franfdez on Sun, 2014-07-27 02:16
Category: 
Loop Modeling

Dear all,

I am trying to use one of the example scripts mentioned in the paper that first described the SWA method for protein loop building [Das, R. (2013). Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. PLoS ONE 8, e74830], but it has been failing on me for reasons I do not understand.

The script is:

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Rosetta 3 - Applications

What build to download?

Submitted by ajasja on Wed, 2014-06-18 09:10
Category: 
PyRosetta

In the list of full releases there are a number of newer files than what is listed on the pyrosseta.org/dow.

Are these also stable releases?  What does the monolith mode mean? (as in mode=release.branch=release.monolith.html)  And what is the namespace mode?

Thank you for satisying my curiosity,
Ajasja Ljubetič

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