VMD-L Mailing List
From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Tue Sep 28 2004 - 07:28:15 CDT
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Hi all?
I would like to calculate rmsd during a simulation. I
used a tcl script before. I would like to modify it
such that it can align first the backbone of a
residue, then it calculate the rmsd of the sidechain
of the residue. I tried to do it by altering the
script that I am going to copy and paste here but I
could not succeed it. Do you have any suggestion about
it?
The script that I was trying to change:
----------------------------------------
set reference [atomselect top "selection " frame 0]
set num_steps [molinfo top get
numframes]
set compare [atomselect top
"selection"]
for {set i 1} {$i <= num_steps} {incr
i} {
set trans_mat [measure fit $compare
$reference]
$compare frame $i
$compare move $trans_mat
set rmsd [measure rmsd $compare
$reference]
puts "RMSD of $i is $rmsd"
}
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- Next message: Manuel Rueda: "Phosphate mass"
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- Reply: lug2002_at_med.cornell.edu: "Re: rmsd calculation and alignment"
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