VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 10 2010 - 16:43:43 CST

Irene,
  Two things to check:
1) Does your DCD file have the cell data intact?
2) Try loading just the PSF and DCD, skip the PDB as the PDB may not
   have a correct periodic cell size

Cheers,
  John

On Wed, Feb 10, 2010 at 12:35:17PM -1000, Irene Newhouse wrote:
> When I run an ILS I've set up using VMD, an early message I get asks if
> I've forgotten to set up PBC because certain coordinates are 0. However,
> looking carefully at all the options for generating the command file for
> an ILS run, I can't figure out how to alter that. However, the run
> continues beyond that. What I don't know is if the results will be
> meaningful - a run hasn't completed yet. I've just pared down a dcd file
> to finish in a couple of days on my best available linux box... Am I
> missing something? I loaded a pdb, a psf & a dcd file into VMD for the ils
> tcl run script creation.
>
> Thanks!
> Irene Newhouse
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078