VMD-L Mailing List

From: gaurav nandrajog (gauravnjog_at_gmail.com)
Date: Tue Sep 09 2008 - 01:01:33 CDT

respected Sir,
          whenever i load my molecule in vmd it suddenly disappears without
any message. i am using vmd 1.8.6 in red hat linux 4. i tried a lot of
things but didnt find anything. plz help me out.

On Mon, Sep 8, 2008 at 10:11 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Rabab,
> How did you get the min/max coordinates that you used in the command
> you specified below? Those coordinates are clearly quite a ways
> away from the lone water that you began with. I believe that the sole
> reason for your problem is that you're specifying min/max coordinates
> that are offset from your original water. How did you input the min/max
> coordinates originally?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Sep 02, 2008 at 08:35:50PM -0700, Rabab Toubar wrote:
> > hi,
> >
> > I was solvating a water molecule with water as a solvent. The command I
> used was :
> > package require solvate
> > solvate water.psf water.pdb -o water_solv -s WT -b 2.4 -minmax {
> {-4.597000002861 16.4689998627 0.34399995804} {32.6819992065 52.2010002136
> 30.9549999237}}
> >
> > Checking the produced pdb file (water_solv.pdb:
> > http://www.uploading.com/files/AFLHVFZN/water_solv.pdb.html
> > I found out that the initial water molecule was outside the solvent box
> and the minmax coordinates were differnet than the input coordinates.
> > I was wondering is there a need to "Translate" the initial water molecule
> before using it in NAMD?
> >
> > Thanks
> > Rabab
> >
> > --- On Tue, 9/2/08, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > From: John Stone <johns_at_ks.uiuc.edu>
> > Subject: Re: vmd-l: solvating a water molecule
> > To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> > Cc: vmd-l_at_ks.uiuc.edu
> > Date: Tuesday, September 2, 2008, 5:16 PM
> >
> > Hi,
> > It's not clear what you did that's giving you the behavior
> > you are describing. Your statements are too vague to interpret.
> >
> > In order for anyone to help you, we would need much more
> > detail about what steps you followed and what the result looks like.
> > It's typically a good idea to provide a link to a URL that contains
> > the structure files from each stage of preparation, and the final
> > result that exhibits the problem(s).
> >
> > Don't email your structure files to the list, just post them on the
> > web somewhere and include a URL.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Sep 02, 2008 at 11:54:47AM -0700, Rabab Toubar wrote:
> > > Hi,
> > >
> > > I am solvating a water molecule, and I always get the original water
> > molecule outside the water box, and accordingly the water box dimensions
> are
> > different than the input. Would the position of the initial molecule
> affect the
> > rest of NAMD simulations? Or it is just a vmd visualization error ?
> > >
> > > Thanks
> > > Rabab
> > >
> > >
> >
> > --
> > 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/ <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
> >
> >
> >
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>