From: Abir Ganguly (aganguly_at_mpi-muelheim.mpg.de)
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 Germany
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