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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...

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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:

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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

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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

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undefined symbol: ZN9CifString12UnknownValueE error meaning?

Category: 
Structure prediction

Hello,

I am trying to run mp_domain_assembly protocol via the cluster and getting this error:

/truba/home/aniyaz/softs/rosetta/main/source/bin/mp_domain_assembly.mpi.linuxgccrelease: symbol lookup error: /truba/home/aniyaz/softs/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libcore.2.so: undefined symbol: _ZN9CifString12UnknownValueE

After several same rows it ended up with the Exit code: 127

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What is virtual atom means in a params file and how to generate it?

Category: 
Compilation

Greetings,

        I'm learning Rosetta now, when I browse the files, I find that Rosetta's database stores some params files, like 1.3.5_trisbromomethylbenzene_symm.params (in /Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker), it contains several V* atoms, and I have trouble understanding the meaning of it. There is also a non-symmetric version of it, named 1.3.5_trisbromomethylbenzene.params, but it still contains virtual atoms. 

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Save silent results to individual directory by process ID

Category: 
Docking

Hi all,

I'm running the docking_protocol application by mpirun, and I want to save silent results to individual directories determined by process ID. 

I found the option "-out:path:mpi_rank_dir" may be helpful but it didn't work. How do I use this option properly? 

 

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