|
|
aarexAmber.pl
From MMTSB
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]
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