From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 03 2010 - 14:47:55 CDT

Hi,
  You'll almost certainly get a much better response by asking
NAMD-specific questions on one of the NAMD mailing lists.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 03, 2010 at 09:48:10AM -0400, Stefan Franzen wrote:
> I have tried to apply the directions provided in the User Guide to use
> colvar. I am using the ubiquitin tutorial as a starting point. In fact,
> you might say I am developing a tutorial section for colvar, which I would
> be happy to make available (once I figure it out). I am quite frustrated
> trying to apply the instructions. the "distance" works fine. But, the
> next step for me of RSMD does not work no matter what I do. Here are two
> things that I have tried. I have included my working file, which just
> tracks the distance between the ends of ubiquitin as an example.
>
> # option 1: put in the atom numbers #
>
> colvar {
> rmsd {
> atoms { 1 2 3 }
> refPositionsFile ubq_ws.pdb
> }
> }
>
> # option 2: put in the C-alphas #
>
> myatoms {
> # add all the C-alphas within residues 1 to 76 of segment "U"
> psfSegID U
> atomNameResidueRange CA 1-76
> }
>
> colvar {
> rmsd {
> atoms { myatoms }
> refPositionsFile ubq_ws.pdb
> }
> }
>
> Thank you,
> Stefan
>
> --
> Stefan Franzen
> Professor of Chemistry
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-515-8915

-- 
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