From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Tue Sep 28 2004 - 07:28:15 CDT

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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