Re: Calculating RMSF per residue

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Apr 20 2015 - 15:59:23 CDT

You may want the VMD mailing list rather than NAMD. Also the VMD manual
lists that there is a built-in rmsf measure function, which may give you
most of what you want (it is per atom, but you can average those results on
a per-residue basis)

On Mon, Apr 20, 2015 at 1:58 PM, Abir Ganguly <aganguly_at_mpi-muelheim.mpg.de>
wrote:

> 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
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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