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

Submitted by zoey on Fri, 2012-09-21 07:15

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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Rosetta 3 - Build/Install

RosettaDock - Constraints File

Submitted by edpryor on Wed, 2012-09-19 06:23

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

Submitted by rlwoltz on Tue, 2012-09-18 17:44

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

Submitted by rlwoltz on Tue, 2012-09-18 14:04

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

Submitted by skovacs on Tue, 2012-09-18 13:49

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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Rosetta 3 - Applications

Backrub Params Files

Submitted by protos_heis on Tue, 2012-09-18 06:15

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

Submitted by lihowe on Sat, 2012-09-15 20:27

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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D070_Refinement.py

Submitted by thorx020 on Fri, 2012-09-14 06:40

Hi,

I'm trying to understand the D070_Refinement.py code posted by the Gray lab on PyRosetta.org. In short, the code basically makes small stabilizing backbone perturbations and repacks the sidechain of random residues in your pose. However, I don't know how many residues get perturbed/repacked. What input parameter specifies the # of residues that get perturbed? The "cycles" parameter is set 9 and is fed to the RepeatMover() function and the comments say that "cycles" affects the amount of sampling, but I'm not don't think think this is what I'm looking for.

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Folding and Docking using Symmetry

Submitted by danielles on Wed, 2012-09-12 11:32

Recently I was trying out the modes of Docking and Fold and Dock using symmetry, but I found that when I got the structures out, none of them were in the native form. The native structure is a dimer with 2 parallel monomers, but all of the structures had the 2 monomers in an antiparallel conformation. In order to understand where I went wrong I went back to the integration test to try it out, but I got antiparallel structures when creating this as well. I wanted to know if I was doing something wrong, had the wrong form of symmetry chosen, what it could be.

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