VMD-L Mailing List

From: srinivasa murthy (srim729_at_yahoo.co.in)
Date: Wed Sep 24 2003 - 08:54:13 CDT

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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