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