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fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz

Category: 
Structure prediction

Hi,

When I run fragment_picker, it gives the message:

ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
ERROR:: Exit from: src/protocols/frag_picker/VallProvider.cc line: 17
 

the detail message as follows:

Post Situation: 

Post-traslational modifications

Category: 
Chemically Modified Residues

Hello, everyone

I was trying to study the effect of post-translational modifications on the structure of proteins. For that purpose, I followed two different approaches:

  1. I modified the residue with a variant using pyrosetta.rosetta.core.pose.add_variant_type_to_residue. Then, I replaced the original residue with the modified one using pose.replace_residue().

Post Situation: 

Converting all residues to poly-Gly/Ala

Category: 
Enzyme Design

Hey, I am pulling my hair out over this. I am trying to convert all residues in a protein to poly-Gly/Ala (for example 1ae1.pdb) but cannot find the Rosetta function to do so. I am replicating a paper where they included code and output, the output appears to be typical Rosetta output (the .pdbs are like 3tzc___1.pdb) which I am assuming were generated with a Rosetta function.

Post Situation: 

XML validation failing

Category: 
Docking

I am trying to validate a .xml script to be used by rosetta_script application. I copied the .xml file from the paper:  Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein−Ligand Docking. But the valdation fails...

When I run,

validate_rosetta_script.default.linuxgccrelease -parser:protocol crystdock.xml -parser:script_vars sg=input random=0

 

Here is my XML:

Post Situation: 

Error compiling in old macOS El Capitan 10.11.6

Category: 
Compilation

Hi all,

I am trying to compile Rosetta-334 week 45, year 2022 in my old friend Mac Mini with macOS 10.11.6 El Capitan.

I am using the standard command line:

./scons.py bin mode=release -j4

After a few second I've got the following error:

Post Situation: 

Run protein-protein docking parallelly by mpi

Category: 
Docking

I run docking_protocol parallelly by mpi (Command: mpiexec -np 10 $ROSETTA_BIN/docking_protocol.mpi.linuxclangrelease @flag_docking).

But the error below occurred.

[ERROR]

-----------------------------------------------------------------------------

Primary job terminated normally, but 1 process returned.

a non-zero exit code. Per user-direction, the job has been aborted.

Post Situation: 

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