From: menica dibenedetto (domenica.dibenedetto_at_gmail.com)
Date: Wed Mar 09 2011 - 08:32:25 CST

Dear all,
I try to run this code to calculate same distance:
cd /Users/domenica/Desktop/01_DOP
mol load pdb 01_DOP_wat.pdb
mol addfile new01.dcd type dcd
set sel1 [atomselect top "resid 136"]
set sel2 [atomselect top "resname DP0"]
set fil [open distance_136-DOP_1f.dat w]
for {set i 1} {$i < 50} {incr i} {
$sel1 frame $i
$sel2 frame $i
set com1 [measure center $sel1 weight mass]
set com2 [measure center $sel2 weight mass]
set simdata($i.r) [veclength [vecsub $com1 $com2]]
puts $fil " $simdata($i.r)"
}
set sel3 [atomselect top "resid 125"]
set sel4 [atomselect top "resname DP0"]
set fil [open distance_125-DOP_1f.dat w]
for {set i 1} {$i < 50} {incr i} {
$sel3 frame $i
$sel4 frame $i
set com1 [measure center $sel1 weight mass]
set com2 [measure center $sel2 weight mass]
set simdata($i.r) [veclength [vecsub $com1 $com2]]
puts $fil " $simdata($i.r)"
}
quit

I run this code inside the TKconsole and it work even if it stopped before
50 frames.
The problem is that I need to run it from command line, but from command
line, the script don't work.
In the output file it wrote only first three distances, and after is repeted
until the and the same distance.
Seems to appen that it don't recognize the different frames.

Best regards,
Domenica