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Docking failure

I'm trying to dock 2 proteins in Rosetta dock serve (http://rosettadock.graylab.jhu.edu/) but it always has this problem:

This job failed to produce results. The RosettaDock Server support team has been notified.

Most failures result from departures from the PDB standards in the input file or from missing or spurious atoms. Please inspect your input file for irregularities and contact us if you need further support.

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ERROR - PDB's with occupancy field equal '1.0'

I've tried to dock 2 protein in Rosetta dock serve (http://rosettadock.graylab.jhu.edu/) but it always has this problem:

Occupancy Error: Submitted PDB(s) have occupancy field other then '1.0'. Currently we only accept PDB's with occupancy field equal '1.0'. Please fix occupancy field and resubmit the job.

Even when I change all the '0.00' value to '1.00' value. Please check my files to see what happen ?
Thank you very much.

P/S: I change the extension of my file from .pdb to .txt

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Rosetta 3.4 on Ubuntu 12.04 - g++-4.6 not found

Hi Rosettaers,

I am building Rosetta 3.4 on Unbuntu 12.04 running in VMWare player. I got the following error when I built it with scons bin mode=release:

Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git
Done. (0.1 seconds)
scons: done reading SConscript files.
scons: Building targets ...

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RosettaDock - Constraints File

Hello, again.

I am attempting to run some global docking simulations of two proteins. Not much is known about the interaction; however, I do know residues that are not involved in forming the protein-protein interface. Is there a way to put this information into a constraints file so that decoys that use these residues are not considered (or thrown out)?

I know that having the line:
SiteConstraint CA 16B A FLAT_HARMONIC 0 1 5

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header pathways not accessable: No such file or directory

I am trying to run a abinitio model and I have a missing header pathway error. My first error I picked up is this when i ran the code from rosetta_demos/abinitio/

core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1

ERROR: [ERROR] invalid header input for kill_hairpins file.
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 375

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Abinitio error: ERROR: Value of inactive option accessed: -in:file:frag9

I hope this isn't a repost but I couldn't find anything here, I found a similar post on minirosetta but it wasn't solved. I built Rosetta and tried to run abinitio in the rosetta_demos using this command /rosetta3.4/rosetta_demos/abinitio$ ../../rosetta_source/bin/AbinitioRelax.linuxgccrelease -in::file::fasta ./input_files/1elwA.fasta

this is my script:
core.init: Mini-Rosetta version unknown from unknown
core.init: command: ../../rosetta_source/bin/AbinitioRelax.linuxgccrelease -in::file::fasta input_files/1elwA.fasta

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Abinitio (3.4) Error: no fragment to compute secondary structure

Greetings,

When trying to run AbinitioRelax in Rosetta 3.4, we obtain the following error message:

ERROR: no fragment to compute secondary structure
ERROR:: Exit from: src/core/fragment/SecondaryStructure.cc line: 68

However, the fragment files seem to be read in correctly, based on the following output:

core.init: Mini-Rosetta version unknown from unknown

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Backrub Params Files

I apologize in advance if this has been answered somewhere else, but I'm having trouble running the backrub program with non-canonical amino acids. Our designed protein includes a chromophore and I constructed a .params file that works with the fixbb application but I can't get backrub to recognize it. I tried renaming one of the atoms to act as a C-alpha for the pivot moves but it still doesn't work. I was just wondering if anyone knows how to get the .params files to work with backrub or if this is even the right was to recognize non-canonical amino acids.

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The problem of compiling omp in Rosetta 3.4

When I execute the command:
./scons.py -j? extras=omp bin mode=dubug
I get the following error:
build/src/release/linux/2.6/64/x86/gcc/4.3/omp/libprotocols_a.2.so: undefined reference to `boost::this_thread::disable_interruption::disable_interruption()'
build/src/release/linux/2.6/64/x86/gcc/4.3/omp/libprotocols_a.2.so: undefined reference to `boost::detail::get_current_thread_data()'
build/src/release/linux/2.6/64/x86/gcc/4.3/omp/libprotocols_a.2.so: undefined reference to `boost::thread::~thread()'

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