latrex.pl - Revision history

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Options

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Edit: /* Description */

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Description

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@@ Line 39: / Line 39: @@
 ; -simopt key=val[,...] : MONSSTER simulation options
 ; -l refPDB min&#58;max[=...] : limit sampling to residue range while keeping rest of the structure restrained to reference PDB
-; -d force res1&#58;res2[=...] : residue-
+; -d force res1&#58;res2[=...] : residue-residue contact restraints
 == Examples ==

@@ Line 30: / Line 30: @@
 ; -help : usage information
+; -n runs : number of replica exchange runs
 == Examples ==

@@ Line 8: / Line 8: @@
 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
+[[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 <docmark>rexserver.pl</docmark><font color=#508060> -monsster</font>.<BR>
+started manually with [[rexserver.pl]]<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
+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
+(see [[latticesim.pl]] 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>
+with <B>-simopt</B>. Finally, as in [[latticesim.pl]]
 distance restraints to be applied during the simulations can be given with
 <B>-d</B>.

←Older revision		Revision as of 22:52, 7 January 2009
Line 1:		Line 1:
−	~~dummy~~	+	__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>

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