VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Jul 28 2007 - 15:36:02 CDT

Okay, so there are two versions of the same script, one in the vmd tutorial,
and one in the namd tutorial. The problem is, the one in the vmd tutorial
(rmsd-fullthrottle.tcl) is hard-coded to work only for ubiquitin (it
specifically references chain U). It also doesn't output anything to a
file. Furthermore, rmsd-fullthrottle.tcl adds a couple lines wrapping the
proc so that you can call it without any arguments.

Your protein likely doesn't have a chain U so the selection it makes in the
script is empty.

The solution: use residue_rmsd.tcl provided in the namd tutorial. It can be
found here:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/2-1-rmsd/

After sourcing the script, you call it as recommended in the namd tutorial.
The script does assume your protein of interest only contains one segment;
this works for most cases, usually unless you are working with multi-protein
complexes.

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Irene Newhouse
Sent: Friday, July 27, 2007 3:17 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: problem with rmsd-fullthrottle

I load my psf file & my dcd file into vmd & open a Tk console. I type
source residue_rmsd.tcl and follow it by

set sel_resid [[atomselect top "protein and alpha"] get resid

A set of numbers spits out.

I then type

source rmsd-fullthrottle.tcl

I get a blue message saying "Calculating rmsd for frame 0..."
Shortly thereafter a red message comes up "measure rmsd: no atoms selected".

However, if I type echo $sel_resid, I get the list of numbers that was
printed to the console from the sel_resid command.

If I try to add sel_resid to the line calling rmsd-fullthrottle, w or w/out
the leading $, I get a message about wrong arguments.

If I do as recommended on
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node1
3.html & type

rmsd_residue_over_time top $sel_resid

I get the same blue & red messages.

There are no new files containing data from any of these attempts. What
should I do?

Thanks!
Irene Newhouse
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