~ demo input for addles
~
~ addles input file for leucine dipeptide
~ this makes a topology and coordinate file usable by SANDER
~
~ open input topology file
~
file rprm name=(leu.dipep.prm) read
~
~ open input coordinates and velocities
~
file rcvd name=(equ.crd) read
~
~ open output topology
~
file wprm name=(les.prm) wovr
~
~ open output coordinates
~
file wcrd name=(les.equ.crd) wovr
~
~ all done with files, start processing commands
~
action
~
~ first copy the leucine residue, 5 times
~
spac numc=5 pick chem mono LEU done 
~
~ now  make an extra 2 copies of the atoms
~ 14-23 (original numbering), just to check multi-level subspacing
~ 
~ this means each of the copies from above will have 
~ 2 copies made, resulting in 10 total copies
~ of this section of the side chain
~
spac numc=2 pick #prt 14 23 done
~
~ this end line needs to be present!
~
*EOD