VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Thu Feb 14 2008 - 08:19:08 CST

I ran into same problem last fall and found taht you have to check your
atom selection and compare to what the RMSD trajectory tool has under

options->backbonedef

default is C Ca N atoms
you can redefine backbone as C Ca N O atoms

the command line options for backbone I believe are C Ca N O
other than that it worked fine for protein and for DNA

On Wed, 2008-02-13 at 17:18 +0100, Jorgen Simonsen wrote:
> Hi,
>
> I get different results when I use the RMSD Trajectory tool and my
> script below - both of them should align to a reference structure and
> then compute the RMSD. The problem is that I get different numbers
> depending on which method I use - I would expect them to be
> identical..
>
> VMD Script
> 0.310802847147 0.334529817104
>
>
> Any help or comments appreciated
> Thanks in advance
>
> Best
> J
>
>
> proc print_rmsd_through_time {{mol top}} {
> # use frame 0 for the reference
> set reference [atomselect $mol "protein" frame 0]
> # the frame being compared
> set compare [atomselect $mol "protein"]
>
> set num_steps [molinfo $mol get numframes]
> for {set frame 0} {$frame < $num_steps} {incr frame} {
> # get the correct frame
> $compare frame $frame
>
> # compute the transformation
> set trans_mat [measure fit $compare
> $reference]
> # do the alignment
> $compare move $trans_mat
> # compute the RMSD
> set rmsd [measure rmsd $compare $reference]
> # print the RMSD
> puts "RMSD of $frame is $rmsd"
> }
> }
>
> print_rmsd_through_time 

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