The problem hasn't been solved
I hate to add another thread about compiling Rosetta with MPI, but after searching through this forum, and trying a number of potential solutions, I am still stuck.
When I execute the command:
$ ./scons.py bin mode=release extras=mpi
I get the following error:
Hi,
I read a single-residue pose stored in pdb file with "pose_from_pdb". Rosetta automatically added the terminus (OXT and two hydrogen atoms). Is there any way to prevent terminus adding or popping them off after reading in?
Thanks,
xfliu
Hi all:
I have got a protein model with clashes in several peptide bonds between O and N atoms, proline residues and some side chanis. The "relax" app removed clashes in the side-chain, but was not able to correct the peptide bonds and proline residues. The following are the options that I used in both fast and throrough runs of the app:
relax.linuxgccrelease -database /home2/rosetta_database -in:file:s 8nC.pdb -relax:fast(thorough) -score:weights score12_full -ex1 -ex2 -nstruct 10
Hi
I'm trying to use the make_fragments.pl script but i do not know where to find the launch_on_slave_strict.py script necessary to run it in parallel, to launch the job serially dosen't seem to be feasible. please see
# This is an optional script that you can provide to launch picker and pdb2vall jobs on
# free nodes to run them in parallel. If left as an empty string, jobs will run serially.
# Make sure your script will run the command passed to it on another machine. If it is
# set up to run parallel jobs on the local machine, the local machine may run into CPU
Hey everyone, I'm trying to compile in mpi mode on a cluster. I used:
./scons.py bin mode=release extra=mpi
After entering the command, it gave me this error:
Running versioning script ... fatal: Not a git repository
But the compiling went on well and gave me "scons: done building targets." at the end.
"yes it runs!" was a really early response for the comparative modeling run I started for a multi chain protein. I use rosetta 3.4.
My problem is that the end result looks completely off compared to the template file (also to any other folded structure, the end result is basically a stretch of amino acids). Points that I messed up something at the alignment.
Hi all, I'm relatively new to this suite (in fact, I've come here from Rosetta 3.4...which I was not successfully able to run...). I installed PyRosetta becuse it had a native Windows installer, and here I am.
What exactly does the filter ddg compute? Does it compute the difference in binding energy from the sequence of the given pose to a mutant? What mutant (perhaps poly alanine)?
I ask because it is somehow different from a binding score (complex minus separated chians), but I'm not sure how.
Dear all,
I would like to use the flag -minimize_sidechains with a symmetric pose in fixbb. At the moment, fixbb stops after
core.pack.task: Packer task: initialize from command line()
ERROR: !core::pose::symmetry::is_symmetric( pose )
ERROR:: Exit from: src/core/optimization/AtomTreeMinimizer.cc line: 72
fixbb runs fine without the -minimize_sidechains flag. Therefore I think I need to include the src/protocols/moves/SymMinimizeMover.cc, as pointed out here at the bottom of the page:
