latrex.pl

Usage

usage:   latrex.pl [options] [files]
options: [-n runs]
         [-par initruns=value,equilruns=value,
               [no]save,savebestfreq=value,archive,
               [no]rebuild,ensmode=add|replace,
               natpdb=file,seq=file]
         [-temp nwin:min:max]
         [-condfile file]
         [-input pdb|chain]
         [-f listfile]
         [-simpar ncycle=val,icycle=val,
                  stiff=val,short=val,central=val,kdcore=val]
         [-simopt limforce=value,gridsize=value]
         [-l refPDB min:max[=min:max ...]]
         [-d force res1:res2[=res1:res2...]]
         [-dir workdir]
         [-ens tag] [-ensdir dir]
         [PARALLELoptions]
         [-log file]

Show source

Description

This script is used to run replica exchange lattice Monte Carlo simulations with MONSSTER. Most of the options are identical to the options in aarex.pl. This script will also start up a server automatically in most parallel environment or can connect to a server that has been started manually with rexserver.pl -monsster.

Input files may be given as in aarex.pl but can be either in PDB or SICHO chain format. The format has to be specified with -input. If no input files are given, random initial conformations are generated.

Lattice simulations require a sequence file that needs to be identified by using the seq parameter in the -par option. The parameter rebuild also only applies to lattice simulations and controls whether the final lattice chains is automatically rebuild to an all-atom model. Depending on the length of each Monte Carlo cycle this may slow down the overall simulation time quite significantly since it is done by the server in a serial fashion.

Lattice simulation specific parameters are set with -simpar (see latticesim.pl for a detailed explanation). The lattice grid size and restraint force constant for loop modeling may be given with -simopt. Finally, as in latticesim.pl distance restraints to be applied during the simulations can be given with -d.

Options

-help 

usage information

-n runs 

number of replica exchange runs

-par key=value[,...] 

replica exchange simulation parameters

-temp nwin:min:max 

number and range of temperature replicas

-condfile file 

conditions file

-input pdb|chain 

input format of initial structure(s)

-f listfile 

list of initial files for different replicas

-simpar key=val[,...] 

MONSSTER simulation parameters

-simopt key=val[,...] 

MONSSTER simulation options

-l refPDB min:max[=...] 

limit sampling to residue range while keeping rest of the structure restrained to reference PDB

-d force res1:res2[=...] 

residue-residue contact restraints

-dir directory 

data directory

-ens tag 

ensemble tag for storing structures sampled at lowest temperature

-ensdir dir 

ensemble directory

-log file 

ouptut log file

Examples

latrex.pl -n 8 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6
performs 8 cycles of replica exchange Monte Carlo lattice simulations with 2 initilization and 2 equilibration runs. The sequence file is required as input parameter and used to generate random input chains. 4 exponentially spaced temperature windows from 1 to 1.6 are used.

latrex.pl -n 8 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -ens rex -ensdir data
runs replica exchange lattice simulations and stores the structures from the lowest temperature window in an ensemble.

latrex.pl -n 8 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -input pdb 1vii.sample.?.pdb
runs a replica exchange lattice simulation starting from SICHO chains that have been generated from the given PDB input files rather than a random chain, generated by default.

latrex.pl -n 8 -par initruns=2,equilruns=2 -par seq=1vii.seq,rebuild,natpdb=1vii.exp.pdb -temp 4:1.0:1.6 -l 1vii.exp.pdb 10:21 -simopt limforce=2.0
runs replica exchange lattice simulations for a loop modeling application. The residues outside the loop are restrained during the simulation with a force of 2.0. The resulting chains are automatically rebuilt at each cycle and since the native structure is given, RMSD values between the reconstructed all-atom structure and the native structure are also calculated and stored.

latrex.pl -n 10 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -hosts sgi.workstations
runs a distributed replica exchange lattice simulations. The host information is taken from sgi.workstations.

latrex.pl -n 10 -par initruns=2,equilruns=2,seq=1vii.seq -temp 4:1.0:1.6 -mp -hosts sgi.local
runs a distributed replica exchange lattice simulations with local directory. The host information is taken from sgi.local.