Dear Tristan,

If we want to calculate COM for whole ligand what should we do in this situation? can we follow this script:

set sel [atomselect top "segid  N1"]

$sel set {x y z}

set coorlist [$sel get {resid x y z}

foreach coor $coorlist {

puts "Residue [lindex $coor 0]: [lrange coor 1 3]"

}

what i need is the COM graph across the time scale (ns)

their is some problem with this code, 

% source com.tcl

wrong # args: should be "for start test next command"

the error is in:

for {set i 0} {$i < [molinfo top get numframes]} {incr $i} {

  molinfo top set frame $i

   set com [measure center $sel]

  set thistime [expr $i * (put frame to time conversion factor here)]

  puts $outfile "$thistime $com"

}