The problem hasn't been solved
I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.
It always complaints:
Hello,
I am currently designing ligand-binding protiens, but designs are returned with more mutations than I would like. In order to reduce this number, I currently use the revert_design_to_native app, but I recently read about about the FavorNativeResidue mover. However, I am unsure of the differences in function between the two. I made two small sets of designs with the FavorNativeResidue bonus set to 0.5 and 1.5, and I ran revert_design_to_native on those designs with the same thresholds, respectivley.
source code: rosetta 2016 week 20
compiling: ./scons.py -j10 mode=debug cat=test
error :
Hi,
I am trying to rebuild the structure from unknown residues (UNK). I have the corresponding EM map and sequence but the PDB file is missing some residues and rest is given as "UNK". I am trying to build an all-atom model using Rosetta. Please suggest as Rosetta does not accept any undefined residues. Any input is welcome.
Thanks
Sushree
Hi, I'm having trouble compiling rosetta 3.5 on my Mac (running El Capitan). I've run the compilation with both clang and gcc and with different versions of both, but continue to get the same error. Here's the output:
Hello!
Currentlxz i am running a command like:
mpiexec -np {0} {1}/source/bin/FlexPepDocking.mpi.linuxgccrelease -database {1}/database -s {2} -ex1 -ex2 -out:file:silent {3}.silent -out:file:silent_struct_type binary -pep_refine -nstruct 100 -unboundrot {4}
On 47 cores (so -np 47) with nstruct set to 100. I would expect 100 output energies in the scoing file, however i get 4700. I guess it somehow makes all the 100 simulation on all the nodes.
I am having troule with the Ligand Docking application. I am currently trying to perform a dock using Automatic RosettaLigand Setup (ARLS). I was able to execute the arls.py script, which creates the arls_work directory. However, once I switch to this new directory, I get an error when I try to run the 1_setup.sh script. Here are the error messages I received:
Hi,
First of all, kudos on all the work that goes into PyRosetta - it makes it quite easy to quickly put together custom protocols.
Quick question - How can I create a SnugDock object in PyRosetta? I am using release 2016.18.58680, and I've compiled pyrosetta under Ubuntu 12.04 (the compilation seems fine as I can call lots of rosetta protocols and they work as expected). It doesn't look like pyrosetta is aware of any of the SnugDock code. Here's a code snippet:
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Dear collegues,
I`ve recently read an excellent publication on pKa prediction using the Rosetta scoring function (Kilambi & Gray Biophys J. 2012 10.1016/j.bpj.2012.06.044). However, it turned out that in the recent Rosetta distribution the pH_protocol.<exe> executable mentioned in the Supplementary materials of that paper is no longer available. I am aware of the ROSIE server, but the waiting list there is quite long and also I keep getting unknown errors with my files.
I'm sorry... I'm sure this is just something basic I overlooked but I'm not sure how this is happening since it seems that a basic component is missing....
I have Rosetta compiled with "extras = mpi" and I have OpenMPI installed.
I ran:
(mpirun --mca btl_tcp_if_exclude lo,virbr0 --hostfile hostfile -np 1 /home/starone/Public/Rosetta/main/source/bin/fragment_picker.mpi.linuxgccrelease @flags > frag.out) >& frag.err