From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Tue Sep 02 2008 - 22:35:50 CDT

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
>
>

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