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protein surface design

Submitted by tatsiana.bylund on Sun, 2019-09-15 03:44
Category: 
Design

I'm running FunFolDes on a template and the generated models have very hydrophobic surfaces. They used human-guided design to introduce charged/hydrophilic mutations on the surface. Is there an automatated way to favor charged/hydrophobic mutations on the surface to begin with?

has anyone used https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/AACompositionEnergy for this purpose?

 

thank you!

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Rosetta 3 - General

"Install_dependencies.pl" gives "Aborted" when downloading "nr" database?

Submitted by Danielsebas on Sat, 2019-09-14 08:53
Category: 
Structure prediction
Downloading nr.96.tar.gz... [OK]
Downloading nr.97.tar.gz... [OK]
Downloading nr.98.tar.gz... [OK]
Downloading nr.99.tar.gz... [OK]
Aborting....
Aborted!

Dear Friends - when running "install_dependencies.pl", I get this above error when the script downloads nr database. I ran the script thrice but it gives the same error. Could you please let me know how to solve this issue? The command line I ran is:

 

./install_dependencies.pl standard &> log.log &

 

Thanks

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Rosetta 3 - Applications

How to analyse multiple silent files from "Abinitiorelax" output to find best models?

Submitted by Danielsebas on Tue, 2019-09-10 10:01
Category: 
Structure prediction

Dear freinds,

 

I read more about rosetta and came up with this command line for denovo structure prediction of 382 residue long protein:

I ran it in silent mode.
 

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Rosetta 3 - Applications

How to uninstall and install rosetta using "extras=mpi'?

Submitted by Danielsebas on Sun, 2019-09-08 03:42
Category: 
Compilation

Dear Friends,

 

I compiled rosetta using :

  

./scons.py -j <number_of_cores_to_use> mode=release bin

But, since I have 20 cores, and I want to distribute the runs across all cores, I want to use "MPI" options. Could you please let me know how can I uninstall and install rosetta using "MPI" option? thanks@!

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Rosetta 3 - Build/Install

How to make new VALL database?

Submitted by Danielsebas on Sun, 2019-09-08 02:16
Category: 
Structure prediction

Dear Friends,

When going through the rosetta tutorials, I see that the vall database is old, and I want to build new vall database. 

could you please let me know how to efficiently build new vall database from PDB structures. When I run pdb2vall, it gives me this:

 

./pdb2vall.py 
Usage: pdb2vall.py [options]

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Rosetta 3 - Applications

extract docking pose from ligand docking silent file

Submitted by Ruska322 on Sat, 2019-09-07 05:21
Category: 
Docking

Hi, everyone ! I try to extract the docking pose from a silent file which contains the ligand docking results. Here is my code:

extract_pdbs.mpi.linuxgccrelease -in:file:silent job01.o  -in:file:tags BLS_0092  -extra_res_fa BLS.params -in::file::fullatom -database main/database

and the followings are output warning info:

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Rosetta 3 - Applications

Unable to understand fragment picking tutorial points.

Submitted by Danielsebas on Thu, 2019-09-05 03:44
Category: 
Structure prediction

Dear Friends,

 

I am performing abinitio structure prediciton of a 382 long protein sequence by following the tutorial:

https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction

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Rosetta 3 - Applications

ligand docking with MPI

Submitted by Ruska322 on Wed, 2019-09-04 03:47
Category: 
Docking

Hello,

I'm trying to use rosetta mpi to dock a library of molecules, but I got this error:

mpirun noticed that process rank 1 with PID 26757 on node c1117 exited on signal 6 (Aborted). It seems there is an error in one node and then causes the whole job aborted, so I wonder if there are any parameters to skip the molecules with problems and continue docking. Many thanks !

Best,

Ruska

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Rosetta 3 - Applications

"sparks failed" error when running "make_fragments.pl"?

Submitted by Danielsebas on Tue, 2019-09-03 03:43
Category: 
Structure prediction
-Precision-7920-Tower:make_fragments.pl -verbose myfasta.fasta 
no id specified. parsing filename instead.
cannot parse id from filename so using 't001_'
ID: t001 CHAIN: _
File for psipred not found! Generating from scratch instead.
picking fragments with options:
                       DEBUG: 1
            add_pdbs_to_vall: 
                       chain: _
                     cleanup: 1
             csbuild_profile: 0
exclude_homologs_by_pdb_date: 0
                           f: myfasta.fasta
                   fastafile: t001_.fasta
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Rosetta 3 - Applications

/database folder after running "install_dependencies.pl" size 657 GB?

Submitted by Danielsebas on Tue, 2019-09-03 03:32
Category: 
Structure prediction

Dear Friends,

 

I nearly ran out of space after running "install_dependencies.pl". Among the programs it installs, /database folder whcih includes "nr" sizes up to 657 GB. Can you please let me know if this is possible? 

 

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Rosetta 3 - Applications

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