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loopmodel issue

I am trying to use loopmodel to fold a linear peptide of 216 standard aa (obtained from the only existing data: fasta file, by using either the BuildPeptide or FragmentPicker executables of rosetta3.3).

I first tried "loopmodel.mpi.linuxgccrelease" (in my Open MPI compilation :scons bin mode=release cxx=gcc cxx_ver=4.6" ALL executables are both ".mpi." and non-mpi, which is strange as not all are parallelized) according to the command line:

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Rosetta3.3 enzyme_design errors

Hi all,
Has anyone else experience stability issues with the enzyme_design app compiled with the Intel compilers? I am getting bus errors/seg faults sometimes, but not when I run exactly the same input with a binary binary compiled with GCC.

As a separate I am also coming across this error sometimes:

ERROR: Dispatch error. Arrived at TrieCountPairGeneric with incompatible count pair data!
ERROR:: Exit from: src/core/scoring/etable/etrie/TrieCountPairGeneric.cc line: 473

Has anyone come across this error?

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rmsd and Lrmsd in loop modeling

Hi,

I have a question about output file test_loop_output.fasc in
an example of Cyclic Coordinate Descent loop closure - loop_modeling.py.
Here we have rmsd and Lrmsd, what is the difference?
In manual you can find that Lrmsd is the rmsd of all loops in the reference
frame of the fixed protein structure.
What does it means? What is rmsd?
How to find rmsd for all loop backbone atoms?

Thank you,

Victor

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dun10

Hi,

Just curious if there is or there will be a flag to use Roland's 2010 Rotamer library within Rosetta. We have been replacing the 2008 binaries with data using the 2010 library and then using the 2008 flag, which works well enough. I'm still learning C++, or I would try and implement it myself.

Also, if it does already work within Rosetta, where would I find it within the code, and which level of smoothing was used? (optim, 5%, 20%)? We have been using optim (with the neighbor-dependent ramachandran flag) across most of Rosetta's apps and it seems to work well.

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ERROR: filtered_alignments.size() > 0

I've been successfully running comparative modeling jobs, but when I tried a new template pdb, I got the following error:

ERROR: filtered_alignments.size() > 0
ERROR:: Exit from: src/protocols/comparative_modeling/CMPoseInputStream.cc line: 167

and the program stops.

I am having the darndest time trying to debug this. Has anyone run across this error before?

Thanks,
-jhbrown

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Relax protocol details for Rosetta 3.1

Hi,

I've searched for details of what exactly the relax protocol does. I know that it does "agressive sampling" and basically just minimises the Rosetta energy. Is there anywhere I can get more detail than that? I've looked through the Rosetta publications and many describe different aspects of Rosetta but I haven't found any that describe specific protocols or applications. I understand that these protocols keep evolving and therefore cannot be described "for once and for all" so, is my search in vain?

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membrane protein packing prediction

Hi, fellows:
We have two transmembrane peptide from two separate membrane proteins and we would like to see how they pack. The conformation of helix 1, i.e., tilt angle w.r.t the membrane etc, is determined by NMR. For the second helix, we currently take it as an ideal helix. The tilt angle for helix 2 is also known. This problem is similar to the glycophorin A packing problem addressed in "Toward high-resolution prediction and design of transmembrane helical protein structures".

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