VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 02 2007 - 20:21:47 CDT

Hi Myunggi,
what selection are you using for the alignment? Are there any major
conformational changes occurring during your trajectory? Can you see the
bad fit visually?
Peter

Myunggi Yi wrote:
> Dear VMD users,
>
> I'm using vmd 1.8.5.
> The following is my rmsd calculation script.
> I always get a big rmsd value at some point.
> Obviously this comes from "bad fitting" (checked by visulizing the
> trajectory)
>
> The same result were reprodued by rmsd tool built in the GUI.
> So, I opened Tkconsole, and typed the command manually at the frame.
> Even with a big rmsd value, I couldn't superimposed the frame.
>
> Is this known problem?
> I attached the xmgrace file generated by VMD (rmsd tool).
>
>
> proc rms { sel step file } {
> set fout [open $file w]
> set mid [$sel molid]
> set nf [molinfo $mid get numframes]
> set ref [atomselect $mid "[$sel text]" frame 0]
> set all [atomselect $mid all]
> puts $fout "0 0"
> # rmsd calculation loop
> for { set i 1 } { $i < $nf } { incr i } {
> molinfo $mid set frame $i
> $sel frame $i
> $all frame $i
> $all move [measure fit $sel $ref]
> puts $fout "[expr $i * $step] [measure rmsd $sel $ref]"
> }
> close $fout
> }
>
>
>