VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 08 2008 - 11:41:45 CDT

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/ 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/      Fax: 217-244-6078