Calculating RMSF per residue

From: Abir Ganguly (
Date: Mon Apr 20 2015 - 12:58:24 CDT

Dear NAMD users,

As the subject line of the email suggests, I am interested in
calculating RMSFs per residue of certain MD trajectories. I looked up
some old threads on the NAMD list, and it seems one way to calculate
RMSFs/residue would be to define a dummy atom, set it's coordinates to
the center of a residue, and calculate RMSF of the dummy atom. I tried
to do this with a simple script (so far just the first part):

mol load pdb ionized.pdb
set PHE532 [atomselect 0 "resname PHE and resid 532"]

set mole [mol new atoms 1]
set sel [atomselect 1 all]
$sel set {x y z} {[measure center $PHE532]}

And I get the error:
atomselect: set: 3 data items doesn't match 1 selected atoms.

In fact, I just tried as a check

$sel moveto {2 0 0}

and the coordinates of mole are still {0 0 0}.

I am probably making a very simple mistake, and I will really appreciate
if some of you guys can point it out.

Thanks so much!

Abir Ganguly, Ph. D.
Postdoctral Researcher
Max-Planck-Institut für Kohlenforschung
Kaiser-Wilhelm-Platz 1
D-45470 Mülheim an der Ruhr

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