MMTSB
Tool Set Documentation

aarexAmber.pl

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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 min:max[_force][=...] 
apply a harmonic restraint to all specified atoms in a given range
-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