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helical bundle predict

Submitted by ii_cnr on Fri, 2020-11-13 09:53
Category: 
Compilation
Structure prediction

Hi everyone,

I'm interested in using the helical_bundle_predict method. In this link (https://www.rosettacommons.org/docs/latest/structure_prediction/helical-bundle-predict) it is described as an application but I cannot understand how to make the system install it. It may have something to do with the fact that it is a pilot application, but still it is not clear to me which files I need to modify in order to install it with scons. 

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Rosetta 3 - Build/Install

Error on rna_denovo_setup.py

Submitted by zahra_AZ on Mon, 2020-11-09 02:23
Category: 
Compilation

Dear all,

I got this error when I want to use the rna_denovo_setup.py 

>~/tools/rna_tools/bin/rna_denovo_setup.py -fasta fasta -secstruct_file secstruct -no_minimize -tag glycine_riboswitch -working_res 1-159 -native 3p49_native_RNA.pdb -cst_file constraints -staged_constraints -cycles 20000 -ignore_zero_occupancy false -silent helix0.out helix1.out helix2.out helix3.out helix4.out helix5.out helix6.out helix7.out -input_silent_res 2-9 65-72 16-21 26-31 33-35 54-56 39-42 48-51 81-85 155-159 92-97 101-106 108-110 145-147 114-117 139-142

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Rosetta 3 - General

Unable to successfully compile using Ubuntu 18.04.5 LTS

Submitted by ampperez on Wed, 2020-10-21 09:30
Category: 
Compilation

Hello,

I am currently unable to correclty compile Rossetta in a Ubuntu 18.04.5 LTS system.

The version I am currently using is Rosetta 3.12.

Then try to compile using with the following...

./scons.py -j 4 mode=release bin

The following terminal output and error are given:

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pepspec anchor dock

Submitted by Astghik on Tue, 2020-10-20 05:31
Category: 
Compilation

I type the following command :

/Users/andreserobian/rosetta_workshop/rosetta/main/source/build/src/release/macos/10.14/64/x86/clang/10.0/default/pepspec_anchor_dock.default.macosclangrelease @dock.args -corrections::restore_talaris_behavior

 

 And I get this error:

[FILE]: src/apps/public/pepspec/pepspec_anchor_dock.cc
[LINE]: 500
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: no ref pdbs loaded!

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Rosetta 3 - Applications

Unable to successfully compile using ubuntu virtual machine

Submitted by leo1990 on Mon, 2020-10-12 21:30
Category: 
Compilation

Hello, I am currently unable to correclty compile. I am running a ubuntu virtual machine on win10 (ubuntu 14.04 LTS, GCC version 4.8.4). 

The version I am currently using is Rosetta 3.12.

Then try to compile using with the following...

./scons.py mode=release bin

The following error is given

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Rosetta 3 - Build/Install

Unable to successfully compile using Mac Catalina 10.15.7

Submitted by Cyrrusm on Tue, 2020-10-06 11:23
Category: 
Compilation

Hello, I am currently unable to correclty compile. I am running a macOS Catalina 10.15.7. 

The version I am currently using is Rosetta 3.12 with Mac binaries

I am able to unzip the file and go into the source folder with the following input:

cd Desktop/Rosetta/main/source/

Then try to compile using with the following...

./scons.py -j3 mode=release bin

The following error is given

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Rosetta 3 - Build/Install

I used mpirun/mpiexec and it runs same job 32times

Submitted by leygkn on Mon, 2020-09-21 00:53
Category: 
Compilation

First, I'm sorry for my poor english.

I compiled rosetta applications via mpi options

(/home/ael/Desktop/rosetta_bin_linux_2020.28.61328_bundle/main/source/bin/relax.mpi.linuxgccrelease)

and I tried to use relax application to prepare structure

Then, when i start relax application, my cpus (16cores, 32threads) rus fully and it calculates same calculations 32times

(one output pdbs and 32 scores in .sc file)

how can i solve this problems?

 

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Rosetta 3 - General

Compilation problems

Submitted by Soler on Wed, 2020-09-09 13:30
Category: 
Compilation
Hi. I have had some problems installing Rosetta 3.12, I have downloaded the source version, the zlib1g-dev package, gcc 9.3.0 and python 3.8.2, my operating system is Ubuntu 20.04.1 LTS. The problem is when I compile rosetta:

if I type: ./scons.py -j 2 mode = release bin ... this is the output from the terminal:

~ / rosetta / main / source $ ./scons.py -j 2 mode = release bin
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running Rosetta with MPI

Submitted by rohi on Sat, 2020-09-05 16:06
Category: 
Compilation

Hello,

I am planning to do four different docking (with 200  structures for one of the partner to capture backbone flexibility) with at least nstruct=500. I need to run it by usening several nodes and processors in our cluster.  I tried to compile MPI  in our cluster, but I got an error attached to this post. Could you please guide me how I can solve the error?

 

 

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