aarexAmber.pl

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