MMTSB
Tool Set Documentation

Difference between revisions of "enslatsim.pl"

From MMTSB
Jump to: navigation, search
 
Line 8: Line 8:
 
This script is used to generate structure ensembles from
 
This script is used to generate structure ensembles from
 
multiple lattice simulation runs. Many options are similar
 
multiple lattice simulation runs. Many options are similar
to <docmark>latticesim.pl</docmark>, the script for single
+
to [[latticesim.pl]], the script for single
lattice simulation runs.<BR><BR>
+
lattice simulation runs.<BR>
 +
 
 
The ensemble directory can be given with <B>-dir</B> if it is
 
The ensemble directory can be given with <B>-dir</B> if it is
 
not the current directory. The number of desired runs is specified
 
not the current directory. The number of desired runs is specified
Line 28: Line 29:
 
With the <B>-opt</B> one or more option files can be read in.
 
With the <B>-opt</B> one or more option files can be read in.
 
By default the option file associated with the <font color=#508060>lat</font> tag
 
By default the option file associated with the <font color=#508060>lat</font> tag
is always read if present.<BR><BR>
+
is always read if present.<BR>
 +
 
 
The option <B>-keeptraj</B> is available to save the lattice
 
The option <B>-keeptraj</B> is available to save the lattice
 
trajectory files for later analysis. These files are usually not
 
trajectory files for later analysis. These files are usually not
Line 35: Line 37:
 
probably want to take advantage of parallel architectures for
 
probably want to take advantage of parallel architectures for
 
a larger number of simulations. The parallel options
 
a larger number of simulations. The parallel options
are explained <A HREF="http://mmtsb.scripps.edu/cgi-bin/parallelopt">here.</A><BR>
+
are explained [http://feig.bch.msu.edu/mmtsb/PARALLELoptions here]<BR>
 +
 
 
The remaining options are used to control the lattice simulations
 
The remaining options are used to control the lattice simulations
 
and are kept in a file <font color=#508060>tag.options</font> for later reference
 
and are kept in a file <font color=#508060>tag.options</font> for later reference
 
and subsequent executions of this script on the same ensemble set.
 
and subsequent executions of this script on the same ensemble set.
 
They are very similar to the options in
 
They are very similar to the options in
<docmark>latticesim.pl</docmark> where a more detailed explanation
+
[[latticesim.pl]] where a more detailed explanation
 
can be found.
 
can be found.
 
  
 
== Options ==
 
== Options ==

Revision as of 13:54, 30 July 2009

Usage

usage:   enslatsim.pl [options]
options: [-seq seqFile]
         [-rnd | -chain file | -pdb file]
         [-sa temp] [-const temp]
         [-par tsteps=val,ncycle=val,icycle=val,
               stiff=val,short=val,central=val,kdcore=val]
         [-g gridsize] [-limforce value]
         [-d force res1:res2[=res1:res2 ...]]
         [-l refPDB min:max[=min:max ...]]
         [-[no]compress]
         [-natpdb pdbFile]
         [-opt file[:file]]
         [-dir workdir]
         [-run [from:]to]
         [-keeptraj]
         [PARALLELoptions]

Show source


Description

This script is used to generate structure ensembles from multiple lattice simulation runs. Many options are similar to latticesim.pl, 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 latticesim.pl where a more detailed explanation can be found.

Options

-help 
usage information


Examples

enslatsim.pl -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.


enslatsim.pl -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.


enslatsim.pl -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.


enslatsim.pl -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.