~
~ all file names are specified at the beginning, before "action"
~
~ file to read prmtop
~
file rprm name=(prmtop) read
~
~ file to read coordinates, velocities and box (this is a restart file)
~
file rcvb name=(md.solv.crd) read
~ 
~ file to write prmtop
~
file wprm name=(LES.prmtop) wovr
~
~ file to write coordinates (and velocities and box since they were read in)
~
file wcrd name=(LES.crd) wovr
~
~ now the action command reads the files and tells addles to process commands
~
action
~
~ do not scale masses of copied particles
~
omas
~
~ divide the peptide into 2 regions.
~ use the CCA option to place the division between carbonyl and alpha carbon
~ use the "or" to make sure all atoms in the terminal residues
~ are included since the CCA option places the region division at C/CA
~ and we want all of the terminal residue included on each end
~
~ make 5 copies of first half and only 4 of second half- normally
~ the same number of copies is used, this is just for illustrating how
~ this can be done and to make a more rigorous test
~
~ "spac" defines a LES subspace (or region)
~
spac numc=4 pick #cca 1 4 | #mon 1 1 done
~
spac numc=5 pick #cca 5 7 | #mon 7 7  done
~
~ the following line is required at the end
*EOD