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 #opens the file that has the atoms that are to be restrained
 # if amber inputs do this
 # mol load parm7 parm.file rst7 crd.file
 # if namd inputs do this
 mol load psf psf.file pdb pdb.file 
 
 set all [atomselect top all]
 $all writepdb ./gdp.reference01.pdb
 
 quit

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