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Rosetta 3.4 build error with

Submitted by aork on Tue, 2012-04-17 16:11

I've been trying to build Rosetta 3.4 on Ubuntu 10.04. I've tried compiling with both gcc 4.4.3 and 4.3.4. Both give me the following error:

src/protocols/canonical_sampling/ParallelTempering.cc: In member function 'virtual void protocols::canonical_sampling::ParallelTempering::finalize_simulation(core::pose::Pose&, const protocols::canonical_sampling::MetropolisHastingsMover&)':
src/protocols/canonical_sampling/ParallelTempering.cc:193: error: size of array 'exchange_accepts_' has non-integral type 'std::pair'

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Rosetta 3 - Build/Install

error with fragment_picker.linuxgccrelease

Submitted by jiongzhang on Tue, 2012-04-17 09:07

I got the error message when I run fragment_picker:
rosetta_source/bin/fragment_picker.linuxgccrelease: error while loading shared libraries: libprotocols.so: cannot open shared object file: No such file or directory

I think this is because some part of the software didn't compile right, but I don't know where. Could anyone help me with this?
Thank you very much!

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Rosetta 3 - Applications

Possible documentation error

Submitted by imurch on Tue, 2012-04-17 00:11

Hi,

I just wanted to report what I think is an error in the documentation for versions 3.3 & 3.4.

On the "Using Constraints Files in Rosetta" page, in the function definition for a SPLINE function, the documentation currently says:
"SPLINE: histogram_file_path experimental_value weight bin_size ... If using RosettaEPR knowledge-based potential, replace with EPR_DISTANCE"

According to my reading of the source code (and my experience using it!) there is a field missing in that description. It should read something like:

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Rosetta 3 - General

Energy and RG in the new rosetta3.4 ( like RG_Energy.cc and RG_Energy_Fast.cc )

Submitted by sdg_lab on Thu, 2012-04-12 08:49

Hello

I have a huge database of PDB files and I need to calculate their RG along with their energy(any relevant scoring).
Earlier version of Rosetta had RG_Energy.cc and RG_Energy_Fast.cc type of files which did this kind of job.

Is there something similar for Rosetta3.4 ?
Please advise

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Rosetta 3 - General

symmetric Docking- TRIMER in Rosetta 3.4 ?

Submitted by sdg_lab on Thu, 2012-04-12 04:22

I need to do certain symmetric docking to generate its homodimer and homotrimer and I am using Rosetta 3.4 Symmetric docking to achieve it.

I used the following command to generate homodimers :

./bin/SymDock.linuxgccrelease -docking:dock_ppk -symmetry:symmetry_definition ./sym_def_dimer.dat -symmetry:initialize_rigid_
body_dofs -database ../rosetta_database/ -out:nstruct 2 -out:file:fullatom -s S_00000001.pdb

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Rosetta 3 - General

how to optimize the weights?

Submitted by Lindsay on Tue, 2012-04-10 07:40

Hi,
I found that there are optimize_weights directory in the protocol directory in the rosetta 3.3 and 3.4. What's the function of this protocol and how to use it? I think this is for weights optimization. If I understand correct In this case, if I have 1 more energy term(suppose this term is totally new), how do I use ”optimize_weights“ to optimize the weights? Thank you very much！

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Rosetta 3 - General

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