# vmd script to select and write out the coordinates 
# from a subsection of a molecule in .xyz format.

# load full equilibrated AChE restart
set molid [mol new AChE.gro waitfor all]

# create a selection 
set sel [atomselect $molid {resid 200 327 440}]

# retrieve number of atoms and get the min/max coordinates from the selection
set minmax [measure minmax $sel]
# subtract the coordinates of the lower left front corner.
$sel moveby [vecscale -1.0 [lindex $minmax 0]]
# and shift by 1 angstrom to the middle
$sel moveby {1 1 1}
# box is the size of the selection plus 2 angstrom 
set box [vecsub [lindex $minmax 1] [lindex $minmax 0]]
set box [vecadd {2 2 2} $box]
# update the box size so the pdbfile has that info
molinfo $molid set {a b c} $box

# write out the result
$sel writepdb {triade.pdb}
quit