set all [atomselect top all]
#get the vector v3 needed
set s1 [atomselect top "index 3540"]
set s2 [atomselect top "index 3542"]
set v1 [lindex [$s1 get {x y z}] 0]
$all moveby [vecinvert $v1]
set v1 [lindex [$s1 get {x y z}] 0]
set v2 [lindex [$s2 get {x y z}] 0]
set v3 [vecsub $v1 $v2]


#move all atoms to new coor..
foreach cor [$all get {x y z}] indx [$all list] {
set at [atomselect top "index $indx"]
#by using Matrix routine
$at moveto [vectrans [transvecinv $v3] $cor]
}