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Difference between revisions of "latrex.pl"
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− | + | __NOTOC__ | |
+ | == Usage == | ||
+ | |||
+ | <mmtsbToolUsage cmd="latrex.pl"></mmtsbToolUsage> | ||
+ | |||
+ | == 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 | ||
+ | <docmark>aarex.pl</docmark>. 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 <docmark>rexserver.pl</docmark><font color=#508060> -monsster</font>.<BR> | ||
+ | Input files may be given as in <docmark>aarex.pl</docmark> but can be either | ||
+ | in PDB or SICHO chain format. The format has to be specified with <B>-input</B>. | ||
+ | If no input files are given, random initial conformations are generated.<BR> | ||
+ | Lattice simulations require a sequence file that needs to be identified by using | ||
+ | the <font color=#508060>seq</font> parameter in the <B>-par</B> option. The parameter | ||
+ | <font color=#508060>rebuild</font> 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.<BR> | ||
+ | Lattice simulation specific parameters are set with <B>-simpar</B> | ||
+ | (see <docmark>latticesim.pl</docmark> for a detailed explanation). The lattice | ||
+ | grid size and restraint force constant for loop modeling may be given | ||
+ | with <B>-simopt</B>. Finally, as in <docmark>latticesim.pl</docmark> | ||
+ | distance restraints to be applied during the simulations can be given with | ||
+ | <B>-d</B>. | ||
+ | |||
+ | == Options == | ||
+ | |||
+ | ; -help : usage information | ||
+ | |||
+ | |||
+ | == Examples == | ||
+ | |||
+ | <mmtsbToolExample cmd="latrex.pl" set="/apps/mmtsb/bench/latrex.pl-test/test1"></mmtsbToolExample> | ||
+ | |||
+ | <mmtsbToolExample cmd="latrex.pl" set="/apps/mmtsb/bench/latrex.pl-test/test2"></mmtsbToolExample> | ||
+ | |||
+ | <mmtsbToolExample cmd="latrex.pl" set="/apps/mmtsb/bench/latrex.pl-test/test3"></mmtsbToolExample> | ||
+ | |||
+ | <mmtsbToolExample cmd="latrex.pl" set="/apps/mmtsb/bench/latrex.pl-test/test4"></mmtsbToolExample> | ||
+ | |||
+ | <mmtsbToolExample cmd="latrex.pl" set="/apps/mmtsb/bench/latrex.pl-test/test5"></mmtsbToolExample> | ||
+ | |||
+ | <mmtsbToolExample cmd="latrex.pl" set="/apps/mmtsb/bench/latrex.pl-test/test6"></mmtsbToolExample> |
Revision as of 22:52, 7 January 2009
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]
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
<docmark>aarex.pl</docmark>. 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 <docmark>rexserver.pl</docmark> -monsster.
Input files may be given as in <docmark>aarex.pl</docmark> 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 <docmark>latticesim.pl</docmark> for a detailed explanation). The lattice
grid size and restraint force constant for loop modeling may be given
with -simopt. Finally, as in <docmark>latticesim.pl</docmark>
distance restraints to be applied during the simulations can be given with
-d.
Options
- -help
- usage information
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.