Difference between revisions of "aarexAmber.pl"

Revision as of 02:40, 31 July 2009

Usage

usage:   aarexAmber.pl [options] [files]
options: [-n runs]
         [-par initruns=value,equilruns=value,
               [no]save,savebestfreq=value,archive
               ensmode=add|replace,natpdb=file,partop=file
         [-temp nwin:min:max]
         [-condfile file]
         [-f listfile]
         [-mdpar Amberparams]
         [-mdopt [no]trajout,[no]conslim,
                 limforce=value,limsel=ca|cb|cab|heavy],
                 [no]translate,ambercoor
         [-l refPDB min:max[=min:max ...]]
         [-cons [ca|cb|cab|heavy] ref|self min:max[_force][=...]]
         [-opt optionsfile]
         [-dir workdir]
         [-ens tag] [-ensdir dir]
         [PARALLELoptions]
         [-log file] [-elog file] [-amberlog file]

Show source

Description

This script works very similar to aarex.pl. It adds replica exchange functionality to Amber.

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
-f listfile: list of initial files for different replicas
-mdpar key=val[,...]: Amber simulation parameters
-mdopt key=val[,...]: Amber simulation options
-l refPDB min:max[=...]: limit sampling to residue range while keeping rest of the structure restrained to reference PDB
-cons [ca|cb|cab|heavy] ref|self
-opt file: options file
-dir directory: data directory
-ens tag: ensemble tag for storing structures sampled at lowest temperature
-ensdir dir: ensemble directory
-log file: ouptut log file
-elog file: energy log file
-amberlog file: Amber simulation log file

@@ Line 11: / Line 11: @@
 ; -help : usage information
+; -n runs : number of replica exchange runs
+; -par key=value[,...] : replica exchange simulation parameters
+; -temp nwin&#58;min&#58;max : number and range of temperature replicas
+; -condfile file : conditions file
+; -f listfile : list of initial files for different replicas
+; -mdpar key=val[,...] : Amber simulation parameters
+; -mdopt key=val[,...] : Amber simulation options
+; -l refPDB min&#58;max[=...] : limit sampling to residue range while keeping rest of the structure restrained to reference PDB
+; -cons [ca|cb|cab|heavy] ref|self
+; -opt file : options file
+; -dir directory : data directory
+; -ens tag : ensemble tag for storing structures sampled at lowest temperature
+; -ensdir dir : ensemble directory
+; -log file : ouptut log file
+; -elog file : energy log file
+; -amberlog file : Amber simulation log file
 == Examples ==