From: Sasthi Charan Mandal (
Date: Wed Aug 01 2018 - 03:17:04 CDT

Oh I am sorry. It will be rmsf. So it would be very much helpful for me if
you would provide me the tcl script. I have one script but using this
script I could not get the expected result. Could you please check my
script and let me know what is wrong here?
The script is:
set outDataFile [open rmsf.dat w]
for {set r 491} {$r <= 512} {incr r} {
set sela [atomselect top "resid $r"]
set selb [atomselect top "resid $r"]
$sela frame 0
for {set f 0} {$f<=9990} {incr f} {
$selb frame $f
display update
set val [measure rmsd $sela $selb]
set resid $r
puts $outDataFile "$resid $f $val"
close $outDataFile

On Wed, Aug 1, 2018 at 6:10 AM, Ashar Malik <> wrote:

> The subject of the mail is asking for rmsf where as in the email you say
> rmsd. So which one?
> Rmsd and rmsf can both be obtained using the "measure" command.
> Remember to remove translational and rotational effects from your system
> prior to their use.
> Write back if this doesn't help and an example "script" can be provided.
> On Aug 1, 2018 00:06, "Sasthi Charan Mandal" <>
> wrote:
> I want to calculate the rmsd of each base pair of dna over a specified
> time.. So if anyone have the script I will be thankful to you if you
> provide me.
> Thanks