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Rosetta v3.x on Biowulf

Rosetta Software Logo from Baker Laboratory The Rosetta++ software suite focuses on the prediction and design of protein structures, protein folding mechanisms, and protein-protein interactions. The Rosetta codes have been repeatedly successful in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition as well as the CAPRI competition and have been modified to address additional aspects of protein design, docking and structure.

Rosetta 2.x is also available.

Older Versions

Rosetta 3.5 Documentation

Examples

To run a set of demos, do the following:

[biowulf]$ qsub -I -l nodes=1
[p2]$ mkdir rosetta_demos
[p2]$ cd rosetta_demos
[p2]$ tar xzvf /usr/local/rosetta3.5/helix_demos_3.5.tgz
[p2]$ ./run_demos.sh

The script run_demos.sh will run through common protocols, each taking no more than a few minutes to complete. The input and output will give a good idea on how to use Rosetta 3.x.

Overview

Rosetta v3.5 contains the same core libraries and algorithms as the version 2 series, but is significantly streamlined and simplified. The two major differences are:

An easy way of selecting the version is to use modules. To see the modules available, type

module avail rosetta

To select a module, type

module load rosetta/[ver]

where [ver] is the version of choice. This will set your $PATH variable, as well as $ROSETTA_DATABASE.

The main Rosetta v3.5 executables are:

AbinitioRelax

Performs de novo protein structure prediction

fixbb

Identifies low free energy sequences for target protein backbones

docking_protocol

Predicts the structure of a protein-protein complex from the individual structures of the monomer components

score

Score a structure with the Rosetta energy function

relax

Relaxes a structure into a minimal energy state

loopmodel

Build and score internal loops for homology modelling

In addition, there are protocols for:

Fragment Files

Fragment files can be generated locally using the make_fragments.pl script. This will generate three secondary structure predictions using SAM, Psipred, and Porter.

Fragment files can also be generated at the Robetta Server Site.

Supporting Programs and Scripts

Here are some supporting programs and scripts for streamlining certain tasks:

File Manipulation

Manipulate input and output files

Evaluation

Evaluating Rosetta output

Clustering

Cluster decoys and models

Run as a batch job

Create a batch input file, e.g. 'rosettaRun':

#!/bin/bash
#PBS -N rosetta
#PBS -e rosetta.err
#PBS -o rosetta.log
cd $PBS_O_WORKDIR
module load rosetta/3.5
relax @flags > relax.log

Submit this job using the PBS 'qsub' command. Example:

qsub -l nodes=1 rosettaRun

See here for more information about PBS.

Run as a swarm

Create a swarmfile, e.g. 'rosettaSwarm':

AbinitioRelax @flags -out:file:silent abinito1.out > abinitio1.log
AbinitioRelax @flags -out:file:silent abinito2.out > abinitio2.log
AbinitioRelax @flags -out:file:silent abinito3.out > abinitio3.log
AbinitioRelax @flags -out:file:silent abinito4.out > abinitio4.log
AbinitioRelax @flags -out:file:silent abinito5.out > abinitio5.log
AbinitioRelax @flags -out:file:silent abinito6.out > abinitio6.log
AbinitioRelax @flags -out:file:silent abinito7.out > abinitio7.log
AbinitioRelax @flags -out:file:silent abinito8.out > abinitio8.log

Submit this job using the 'swarm' command. Example:

swarm -f rosettaSwarm --module rosetta/3.5

See here for more information about using swarm.

Run as an MPI batch job

The Rosetta executables have been compiled to utilize MPI. Not every executable can parallelize, but the basic abinitio works well. You will need to load a different module (mpi_*) instead of the default.

Create a batch input file, e.g. 'rosettaRunMPI':

#!/bin/bash
#PBS -N rosettaMPI
#PBS -e rosettaMPI.err
#PBS -o rosettaMPI.log
cd $PBS_O_WORKDIR
module load rosetta/mpi_3.5
mpirun -np 96 -machinefile $PBS_NODEFILE AbinitioRelax @flags
combine_silent -database $ROSETTA_DATABASE -in:file:silent silent_* -out:file:silent silent.out
rm silent_*

The above is an example of a 96-cpu MPI job. You will need to allocate the proper number of nodes and cores to match this value. For example, 4 c24 nodes:

qsub -l nodes=4:c24 rosettaRunMPI

Or 6 c16 nodes:

qsub -l nodes=6:c16 rosettaRunMPI

NOTE:The number of decoys MUST be equal to or greater than the number of processors, as set by the -np option to mpirun. Otherwise the program will exit with errors.

File Manipulation

cat_silent.pl: concatenate silentfiles
changeChain: change the chain id of a PDB
createLoop.pl: create a dummy structure from a sequence of amino acids
createTemplate.pl: create a homology model template from a FASTA file and a homologous structure

Evaluation

VMD: X-Windows molecular graphics viewer
getColumn.pl: display silentfile and scorefile columns
gnuplot: graphically display data
cluster_plot.pl: generate a gnuplot input file to plot the score versus another field
histogram.pl: generate a quick histogram from STDIN data

Clustering

cluster_pdbs.pl: cluster a set of PDBs
cluster_variation.pl: find per-residue variation within a cluster