VMD-L Mailing List

From: Vineet Pande (pande.vin_at_gmail.com)
Date: Sun Jun 04 2006 - 09:53:18 CDT

Hi,
Now I notice that if I load the same trajectoty [but] without solvent
(solvent removed already from a CHARMM trajectory), VMD shows the display of
solute correctly. Still its strange that display is incomplete with a
trajectory containing solvent.

Vineet, 

---
Vineet Pande, Ph.D.
Karolinska Institute, Stockholm
On 6/3/06, Vineet Pande <pande.vin_at_gmail.com> wrote:
>
>  Yes. even if use "nucleic not solvent" or "all not solvent" selection
> while displaying in *default display*; VMD does not show the molecule
> completely.
>
> Vineet
>
> ---
> Vineet Pande, Ph.D.
> Karolinska Institute, Stockholm
>
>
>  On 6/2/06, Leonardo G. Trabuco <ltrabuco_at_ks.uiuc.edu> wrote:
> >
> > On Fri, Jun 02, 2006 at 04:17:51PM +0200, Vineet Pande wrote:
> > > Hi,
> > > I am using VMD for WIN32, version 1.8.4b10 to display a simple CHARMM
> > > trajectory of a nucleic acid duplex. However, in the graphics, I can't
> > see
> > > one of the terminal nucleotides in both the strands; the MD movie runs
> > fine
> > > however. What could be the problem?
> >
> > Are you using the keyword 'nucleic' in your atom selection? Which
> > representation are you using?
> >
> > Leo
> >
> > --
> > Leonardo Giantini Trabuco
> > Ph.D. candidate
> > Center for Biophysics and Computational Biology
> > University of Illinois at Urbana-Champaign
> >
>
>