VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Feb 10 2010 - 17:01:24 CST

Thanks again!

Irene
 
> Date: Wed, 10 Feb 2010 16:59:29 -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
>
>
> An easy way is to query it via molinfo, e.g.:
> molinfo top get { a b c alpha beta gamma }
>
> If you get a/b/c lengths of zero, or one, or some other nonsense value,
> that'd indicate trouble.
>
> Cheers,
> John
>
> On Wed, Feb 10, 2010 at 12:53:43PM -1000, Irene Newhouse wrote:
> > 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
> > > >
> > > > ----------------------------------------------------------------------
> > > >
> > > > Hotmail: Powerful Free email with security by Microsoft. Get it now.
> > >
> > > --
> > > 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
> >
> > ----------------------------------------------------------------------
> >
> > Hotmail: Powerful Free email with security by Microsoft. Get it now.
>
> --
> 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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