VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 23 2003 - 10:04:39 CDT

Dear Srinivas,
  Try running the script in a freshly started VMD _without_ TkCon.
There's a known conflict between the "alias" command in TkCon and
one in psfgen. Its likely that your problem is being caused by this
conflict. Run the same script in the regular VMD console and it'll
probably work fine. Try that and let us know the result.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 22, 2003 at 11:40:10PM -0700, srinivasa murthy wrote:
> hi,
> I am new user of VMD. I am using vmd-1.8.1(binary
> for linux). I wanted to create a water sphere of
> radius 10 angstrom . I went
> through vmd-l mailing list and found tcl script for
> the purpose(Re: creating spherical water
> droplet->Justin Gullingsrud ).Script goes like this(i
> have modified slightly..though original one gave same
> result)
>
> package require psfgen
> set rad 10
> set r2 [expr $rad*$rad]
> set wat2delete [atomselect top
> "(sqr(x)+sqr(y)+sqr(z)>$r2"]
> foreach segid [$wat2delete get segid] resid
> [$wat2delete get resid] {
> delatom $segid $resid
> }
> writepsf watsph.psf
> writepdb watsph.pdb
>
> I ran this script after creating a water box using
> solvate -o new -minmax { { 0 0 0} {50 50 50} }
> and loading new.pdb and new.psf to vmd..
>
> I get this output in vmd Tkcon console after the
> foreach loop
> no segment WT1
> no segment WT1
> ..
> ..
> ..
> or if i use only resid in foreach loop
> no segment 4
> no segment 4
> ..
> ..
> no segment 250
> no segment 250
> ..
> ..
>
> but when i use $wat2delete get resid .. i got the list
> of water molecules to be deleted..
>
> what could be the problem
>
> regards
> srinivasa
>
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-- 
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