From: Karol Kaszuba (
Date: Fri Jul 27 2007 - 13:56:22 CDT


   I would like to report some strange problem.

   I performed MD.
   I loaded the PSF file.
   I loaded the DCD file.
   I calculated RMSD for heavy atoms of one SIDECHAIN and I noticed the
   following problem:

   The RMSD value was irrationally high - reached even 350 A.
   The carbon atoms of my sidechain were 300 A away from the protein.
   The hydrogen atoms of my sidechain were "in place" (still constituted a
   part of the protein).

   First I thought that my simulation went abnormally - for example: heavy
   atoms of the sidechain "escaped" and remained separated but they didn't -
   I was observing them during DCD playing.
   It looks like RMSD calculation moves my heavy atoms away from protein.
   Furthermore - when I calculated RMSD for whole resid 37 I obtained a
   correct rmsd value and the heavy atoms of the sidechain were not moved for
   300 A.

  I am using the folowing rmsd.tcl script with the VMD for linux 32, version
  set outfile [open rmsd_37.dat w]
  set nf [molinfo top get numframes]
  set frame0 [atomselect top "protein and resid 37 and sidechain and not
  hydrogen" frame 0]
  set sel [atomselect top "protein and resid 37 and sidechain and not
  # rmsd calculation loop
  for {set i 1 } {$i < $nf } { incr i } {
    $sel frame $i
    $sel move [measure fit $sel $frame0]
    puts $outfile "[measure rmsd $sel $frame0]"
    close $outfile

   I would like to ask if someone know what may cause this problem and how to
   omit it?

   Thank you in advance,


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