VMD-L Mailing List

From: mashaojie163 (mashao_jie_at_163.com)
Date: Tue Sep 28 2004 - 10:46:15 CDT

please tell me the error message, In my opinion, you should write as following: ,in yourt scripts, the command "set trans_mat [measure fit $compare $reference]" should be excuted after the command " $compare frame $i". Maybe you can try

> ----------------------------------------
>
> set reference [atomselect top "selection " frame 0]
>
>
> set num_steps [molinfo top get numframes]
>
>

>
>
> for {set i 1} {$i <= num_steps} {incr i} {
> set compare [atomselect top "selection" frame $i]
                     
>
      set trans_mat [measure fit $compare $reference]
>
>
> $compare move $trans_mat
>
>
> set rmsd [measure rmsd $compare $reference]
>
>
>
> puts "RMSD of $i is $rmsd"
>
> }
>
>
>

    
----- Original Message -----
From: "bora erdemli" <boraerdemli_at_yahoo.com>
To: <vmd-l_at_ks.uiuc.edu>
Sent: Tuesday, September 28, 2004 8:28 PM
Subject: vmd-l: rmsd calculation and alignment

> 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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