VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Feb 10 2010 - 16:53:43 CST

Thank you! How would I check the dcd file for PBC data? I *did* use catdcd to stride it down. I'll also try using just the psf file.

 

Irene
 
> Date: Wed, 10 Feb 2010 16:43:43 -0600
> From: johns_at_ks.uiuc.edu
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: how to set PBC for ILS
>
>
> 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
                                               
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