From: Abir Ganguly (aganguly_at_mpi-muelheim.mpg.de)
Date: Tue Apr 21 2015 - 02:58:40 CDT
Hi Lurong, Aron,
Thanks so much for the quick response (and the script!). Firstly, I
apologize for submitting this email to the NAMD list. I realized it as
soon as I sent my email, but it was already too late.
Lurong, I actually wrote a script to calculate the "RMSF_CA". The
relevant portion (post alignment of the trajectory) is below:
set ref_CA [atomselect 1 "$sel_string”]
set rmsf [measure rmsf $cur_CA]
for {set i 0} {$i < [$cur_CA num]} {incr i} {
puts $outfile [format %12.6f [lindex $rmsf $i]]
}
which is similar to your script. I was actually looking up some old
threads, and one of the threads had this idea of using dummy atoms. I
was just curious why I could not set the coordinates of the dummy atom
in the toy script I posted.
Anyway, thanks so much for your script. I guess I will just go with
Aron’s idea of calculating RMSFs of all atoms and then average it out
over the residues.
Best,
On 04/20/2015 10:59 PM, Aron Broom wrote:
> 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 <mailto: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
-- 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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