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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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Get fasta from PDB script correction - Solved

Category: 
Design

Dear researchers,

Those who really want to use the get_fasta_from_pdb.py script to generate the FASTA files from PDB, generally face some sorts of errors.

The most common error is: TabError: inconsistent use of tabs and spaces in indentation

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Ensemble Docking with RosettaDock 4.0 Protocol

Category: 
Docking

Greetings,

I'm trying to perform an Ensemble Docking using RosettaDock 4.0 as the protocol. The structures were relaxed, and ensembles generated for both proteins. Once the runs start using the MPI version:

$ mpirun -np 24 --hostfile $PBS_NODEFILE docking_protocol.mpi.linuxgccrelease -in:file:s ../input/4udt_AB_prepack.pdb -in:file:native ../input/4udt_xtal.pdb -unboundrot ../input/4UDT_AB_renum_noHET.pdb -nstruct 5000 -ensemble1 ensemble/4udt_A_ensemblelist -ensemble2 ensemble/4udt_B_ensemblelist -partners A_B @dock_ensemble_flags

Post Situation: 

errors about RIFdocking

Category: 
Design

Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. An error occurs when I run the command: Signal 6 (SIGABRT) means that the process was aborted.  This usually means an internal Rosetta error caused by (often)  bad inputs, (sometimes) developer error, or (rarely) hardware problems.
Has anyone encountered this error with Rosetta? How can I solve this problem? I'd be grateful if you could give me any help.

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