Tool Set Documentation

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usage: [options] [files]
options: [-n runs]
         [-par initruns=value,equilruns=value,
         [-temp nwin:min:max]
         [-condfile file]
         [-input pdb|chain]
         [-f listfile]
         [-simpar ncycle=val,icycle=val,
         [-simopt limforce=value,gridsize=value]
         [-l refPDB min:max[=min:max ...]]
         [-d force res1:res2[=res1:res2...]]
         [-dir workdir]
         [-ens tag] [-ensdir dir]
         [-log file]
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This script is used to run replica exchange lattice Monte Carlo simulations with MONSSTER. Most of the options are identical to the options in 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 -monsster.

Input files may be given as in 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 for a detailed explanation). The lattice grid size and restraint force constant for loop modeling may be given with -simopt. Finally, as in distance restraints to be applied during the simulations can be given with -d.


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 -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. -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. -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. -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. -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. -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.