VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 24 2003 - 13:16:05 CDT

Srinivasa,
  No, you don't need to recompile VMD, but you'd need to close VMD,
start a new VMD session, but make sure that you do NOT open TkCon,
as once the TkCon script is read into VMD, its 'alias' command will
conflict with psfgen. If this is indeed what you tried, let me know
and I'll look into your problem more closely.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 24, 2003 at 02:54:13PM +0100, srinivasa murthy wrote:
> hi john,
> I tried to run the script in vmd console, but
> i got same error.
> When you said VMD_without_TKcon,did it mean,
> reinstalling vmd by changing configure.options.
> Correct me if i am wrong.
>
> Regards
> Srinivasa
>
> ----------------------------------------------
> --- John Stone <johns_at_ks.uiuc.edu> wrote: >
> > 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
>
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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