What is Rosetta and Rosetta@home?
Rosetta@home ist ein nichtkommerzielles Projekt, das mittels der Technik des verteilten Rechnens versucht, Proteinstrukturen und Proteinbindungen aus einer Aminosäuresequenz vorherzusagen.
Dabei werden Algorithmen entwickelt und getestet, die eine zuverlässige Strukturvorhersage ermöglichen. Eine akkurate Vorhersage von Proteinstrukturen könnte sich als sehr hilfreich für die Entwicklung von Heilverfahren für beispielsweise AIDS, Krebs, Malaria, Alzheimer und Virenerkrankungen erweisen.
The Rosetta software suite focuses on the prediction and design of protein structures, protein folding mechanisms, and protein-protein interactions. Rosetta has been consistently successful in CASP and CAPRI competitions. Rosetta also addresses aspects of protein design, docking and structure. The software is the foundation for the Human Proteome Folding Project on the World Community Grid and the Roseta@home distributed computing project.
Rosetta Software is free for academic and non-profit users.
Download Rosetta and License Information
Rosetta Software is free for academic and non-profit users.
A license must first be obtained to login and download software.
If you want to use Rosetta on our bwGRID-HPC-System, please:
... or: contact us using this email : rainer.rutka(at)uni-konstanz.de
... we will then contact the user with instructions for using CPMD on our cluster.
We already got an academic license!
- Rosetta Latest Distribution (Bundle 817 MB!): the actual distribution of Rosetta we are running is: 3.3
Installed programs (in /opt/bwgrid/chem/rosetta/3.3/bin)
rosetta_source/bin :- AbinitioRelax.linuxgccrelease
AbinitioRelax.mpi.linuxgccrelease - AnchoredDesign.linuxgccrelease
AnchoredDesign.mpi.linuxgccrelease - AnchoredPDBCreator.linuxgccrelease
AnchoredPDBCreator.mpi.linuxgccrelease - AnchorFinder.linuxgccrelease
AnchorFinder.mpi.linuxgccrelease - antibody_mode.linuxgccrelease
antibody_mode.mpi.linuxgccrelease - backrub.linuxgccrelease
backrub.mpi.linuxgccrelease - benchmark.linuxgccrelease
benchmark.mpi.linuxgccrelease - BuildPeptide.linuxgccrelease
BuildPeptide.mpi.linuxgccrelease - ca_to_allatom.linuxgccrelease
ca_to_allatom.mpi.linuxgccrelease - cluster_alns.linuxgccrelease
cluster_alns.mpi.linuxgccrelease - cluster.linuxgccrelease
cluster.mpi.linuxgccrelease - combine_silent.linuxgccrelease
combine_silent.mpi.linuxgccrelease - CstfileToTheozymePDB.linuxgccrelease
CstfileToTheozymePDB.mpi.linuxgccrelease - ddg_benchmark.linuxgccrelease
ddg_benchmark.mpi.linuxgccrelease - ddg_monomer.linuxgccrelease
ddg_monomer.mpi.linuxgccrelease - design_contrast_and_statistic.linuxgccrelease
design_contrast_and_statistic.mpi.linuxgccrelease - docking_prepack_protocol.linuxgccrelease
docking_prepack_protocol.mpi.linuxgccrelease - docking_protocol.linuxgccrelease
docking_protocol.mpi.linuxgccrelease - enzyme_design.linuxgccrelease
enzyme_design.mpi.linuxgccrelease
- AbinitioRelax.linuxgccrelease
blue = symbolic links
bwGRID Anpassungen / adaptations
Rosetta
| Description: | Configuration - Command line for xxxx |
| Path/Filename: | /opt/bwgrid/chem/rosetta/3.3/rosetta_source/tools/build/basic.settings |
| Description: | Module - File |
| Path/Filename: | /opt/bwgrid/chem/rosetta/3.3/modulefiles/chem-rosetta-3.3 |
| ALL-IN-ONE: | TGZ - Tarball | expand in /opt/bwgrid/chem/rosetta with [tar xvzf] |
| Path/Filename: | /opt/bwgrid/chem/rosetta/rosetta3.3-bwgrid-config.taz |
Build Rosetta parallel mode
To build Rosetta in MPI, simply add extras=mpi to your command line for compiling.
This produced the MPI-enabled "parallel" executables. Note that almost all of Rosetta is not parallel; the Job Distributor layer is parallelized to allow many independent trajectories under the MPI umbrella.
This means you won't get a performance boost from running 100 Rosetta jobs in regular mode versus a 100-processor MPI job.
The executeables ought to have "mpi" in their name somewhere. We created a symbolic link excluding the _mpi suffixes. See ~/bin.
... download : rosetta_source/tools/build/basic.settings
$ cd rosetta_source
./scons.py bin mode=release extras=mpi
bwGRID examples
The PBS batch system can be used to manage the nodes allocation in a cluster of hosts. For example, using a particular job script, it's possible to communicate to the MPI launcher program (mpirun) the number and the list of nodes that PBS has allocated for the whole job as requested from the user. The PBS server will not run more jobs on the busy nodes until the end of the current job. Here is an example of a script to do this over our bwGRID network using an implementation of Open-MPI.
| Description: | bwGRID - Example PBS File for submitting a job via. 'qsub' |
| Path/Filename: | /opt/bwgrid/chem/rosetta/3.3/bwgrid-examples/bw-grid-rosetta3.3-example.pbs |
| Description: | bwGRID - Example data file for tests (abridged) |
| Path/Filename: | /opt/bwgrid/chem/rosetta/3.3/bwgrid-examples/score-example.pdb |
Run Rosetta3.3 test for the relax application...
The 'relax' application in Rosetta carries out the task of simple structural refinement of fullatom Rosetta models. It can also read Centroid models, in which case it will convert the model into a fullatom model and pack the sidechains. Relax does not carry out any extensive refinement and only searches the local conformational space neighbourhood.
See:http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_relax_command.html
for some more explanations and examples.
COMMAND (example)
$ROSETTA3_SRC/bin/relax.mpi.linuxgccrelease \
-database $ROSETTA3_DB \
-score:weights score13_env_hb \
-out:pdb -out:prefix relaxed -out:nstruct 100 \
-in:file:s score-example.pdb
COMPLETE SET OF TESTS
If you built the test patterns using:
$ ./scons.py -j8 cat=test mode=release
you're able to perform a complete set of tests running 'run.py' in the Rosetta source folder [cd $ROSETTA3_HOME/rosetta_source]:
$ python test/run.py -d /opt/bwgrid/chem/rosetta/3.3/rosetta_database -j8 --mode=release
* Always use the fully-qualified-pathname for the database folder!
© Copyright Rosetta Commons Member Institutions
Δ 21.12.2011 | initial version | rainer.rutka(at)uni-konstanz.de
