Tool Set Documentation

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usage: [options]
options: [-seq seqFile]
         [-rnd | -chain file | -pdb file]
         [-sa temp] [-const temp]
         [-par tsteps=val,ncycle=val,icycle=val,
         [-g gridsize] [-limforce value]
         [-d force res1:res2[=res1:res2 ...]]
         [-l refPDB min:max[=min:max ...]]
         [-natpdb pdbFile]
         [-opt file[:file]]
         [-dir workdir]
         [-run [from:]to]

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This script is used to generate structure ensembles from multiple lattice simulation runs. Many options are similar to, the script for single lattice simulation runs.

The ensemble directory can be given with -dir if it is not the current directory. The number of desired runs is specified using -run either followed by a single number for the total number of runs or by an explicit interval.

During lattice simulations a MONSSTER sequence file is needed and has to be provided through the -seq if it has not been given previously and its location is not available from the ensemble configuration file. A reference PDB file for comparison with the native conformation may be given through -natpdb but is not required. For loop or fragment modeling the range of residues that are being modeled and a template PDB file with the structure outside the modeled residues are specified using -l. Like the location of the sequence file and the native PDB structure this data may already be present in the ensemble configuration file and does not need to be given in that case.
With the -opt one or more option files can be read in. By default the option file associated with the lat tag is always read if present.

The option -keeptraj is available to save the lattice trajectory files for later analysis. These files are usually not kept since they require a significant amount of disk space.

Although this script will work in a serial fashion, one would probably want to take advantage of parallel architectures for a larger number of simulations. The parallel options are explained here

The remaining options are used to control the lattice simulations and are kept in a file tag.options for later reference and subsequent executions of this script on the same ensemble set. They are very similar to the options in where a more detailed explanation can be found.


usage information
-seq file 
provide MONSSTER sequence file
start from random chain
-chain file 
initial conformation given as SICHO chain
-pdb file 
initial conformation given as PDB file
-sa temp 
simulated annealing runs from given temperature to 1.0
-const temp 
constant temperature runs at given temperature
-par key=value[,...] 
MONSSTER parameters
-g gridsize 
lattice grid size (should match MONSSTER)
-l refPDB min:max[=...] 
restrict sampling to specified residue range with rest of structure restraint to reference PDB (for loop modeling)
-limforce value 
force constant to be used for restraining structure outside loop region
-d force res1:res2[=...] 
apply pairwise residue-residue contact restraints
(do not) compress output files
-natpdb pdbFile 
provide reference structure for automatic RMSD calculations
-opt file[:file...] 
file with MONSSTER options
-dir directory 
data directory
-run [from:]to 
limit to subset of ensemble
do not delete MONSSTER trajectory files after runs are complete

Examples -dir data -run 5 -seq 1vii.seq -natpdb 1vii.exp.pdb -rnd -par tsteps=10,ncycle=10 -sa 2.0
performs 5 lattice simulation runs and stores them in an ensemble data structure. The ensemble is stored under the data directory. Each lattice simulation is started from a random chain and run with 10 Monte Carlo cycles over 10 simulated annealing steps from a temperature of 2.0 to 1.0 in internal MONSSTER units. -dir data -run 6:20 -rnd -cpus 3
adds more lattice simulation runs for indices 6 through 20 to an existing ensemble in the data directory. The sequence file and native PDB as well as the lattice simulation options are taken from the configuration files. The simulations are run in parallel on 3 CPUs. -dir data -run 5 -cpus 2 -seq 1vii.seq -natpdb 1vii.exp.pdb -l 1vii.exp.pdb 10:21 -limforce 50.0 -rnd -par tsteps=10,ncycle=10,central=0.1 -sa 2.0
generates ensemble structures from 5 lattice simulation runs, run in parallel on 2 CPUs, for a typical loop modeling application. Residues 10 through 21 are simulated against a restrained structure template taken from 1vii.exp.pdb. The maximum restraint force is set to 50.0. Random loop conformations are generated as starting structures. The simulated annealing simulation runs are carried out with 10 temperature steps and 10 Monte Carlo cycles per step. The scaling of the centrosymmetric potential is reduced to 0.1. -dir data -run 10 -seq 1vii.seq -natpdb 1vii.exp.pdb -rnd -par tsteps=10,ncycle=10 -sa 2.0 -cpus 4 -hosts sgi.workstations
performs 10 lattice simulation runs in parallel on 4 cpus distributed onto hosts from sgi.workstations. The ensemble structures are stored under the data directory. Each lattice simulation is started from a random chain and run with 10 Monte Carlo cycles over 10 simulated annealing steps from a temperature of 2.0 to 1.0 in internal MONSSTER units.