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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: 

ARM64 Apple M1Error compiling Rosetta with extras=mpi

Category: 
Compilation

I'm trying to build Rosetta-3.13 "rosetta.source.release-334" with the following command:

./scons.py mode=release bin extras=mpi

I have also updated the site.settings file to prepend the mpicxx and mpicc compilers for openmpi installed in my system.

I got the following error:

ld: warning: ignoring file /opt/programs/openmpi/4.1.4/lib/libmpi.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64

.... lots of lines...

Post Situation: 

Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?

Category: 
Scoring

Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?

So far I thought the soft score function is supposed to feature lower repulsive terms.

ref2015_soft.wts:

Post Situation: 

Error when attempting to relax pdb, "flag_input_relax" not found

Category: 
Structure prediction

I am following the rosetta tutorials and run into an error when attempting to relax a pdb for refinement. The "flag_input_relax" file cannot be opened by rosetta, even though I've granted myself full permissions and even changed it into an executable via chmod 755. I made a copy of the file and it could not open the copy either. Below is the command that gives me the error:

 

rosetta/main/source/bin/relax.default.macosclangrelease -in:file:s ~/rosetta/main/demos/tutorials/input_and_output/input_files/from_rcsb/1qys.pdb flag_input_relax

Post Situation: 

relax protein with multi-conformer bound ligand

Category: 
Small Molecules

I am working with a protein with a bound small molecule (non-covalent). I've managed in creating parameters for the ligand and relaxing the complex following this workflow: https://new.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README

Post Situation: 

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