VMD-L Mailing List

From: Srinivasan Madabushi (smadabushi_at_gmail.com)
Date: Fri Dec 17 2004 - 18:24:44 CST

Hi,
   I am a novice user of VMD, so apologies if my query is stupid.
I am trying to calculate the RMSDs of just the transmembrane region of
a 7 transmembrane receptor. The simulation was of the entire protein
(TM domains + loops). I want to know how to direct VMD to calculate
RMSD's only on non-contiguous regions of interest (eg. 8-28 & 37-61 &
80-101 etc)
I tried the script below but it does not work.. and gives me the RMSD
of the entire protein.
Any help is really appreciated.

Thanks
Sri.

set outfile [open rmsd.dat w]
set nf [molinfo top get numframes]
set frame0 [atomselect top "resid 8 to 28 or resid 37 to 61 or resid
80 to 101 or resid 105 to 126 or resid 133 to 153 or resid 165 to 191
or resid 201 to 225" frame 0]
# rmsd calculation loop
for { set i 0 } { $i <= $nf } { incr i } {
set sel [atomselect top "resid 8 to 28 or resid 37 to 61 or resid
80 to 101 or resid 105 to 126 or resid 133 to 153 or resid 165 to 191
or resid 201 to 225" frame $i]
$sel move [measure fit $sel $frame0]
puts $outfile "[measure rmsd $sel $frame0]"

}
close $outfile