VMD-L Mailing List

From: srinivasa murthy (srim729_at_yahoo.co.in)
Date: Fri Sep 26 2003 - 00:18:41 CDT

Sorry john,
          I had problems with my yahoo account.
Yes, i indeed, tried to run the script from vmd
console
(I typed the commands in vmd console)..and ended up
with same error
  By the way, when i ran script in vmd console(my
script file is bub.tcl)

vmd > source bub.tcl
wrong # args: should be "set varName ?newValue?"

but

vmd > source
wrong # args: should be "source fileName"

i tried the run script in vmd text mode.

[gsmurthy_at_ncsc0 vmd-1.8.1]$ ./vmd -dispdev text -e
bub.tcl
Info) VMD for LINUX, version 1.8.1 (June 15, 2003)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to
vmd_at_ks.uiuc.edu
Info) Please include this reference in published work
using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K.,
`VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996,
14.1, 33-38.
Info)
-------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
1.3.2
wrong # args: should be "set varName ?newValue?"
wrong # args: should be "set varName ?newValue?"
can't read "r2": no such variable
can't read "wat2delete": no such variable
Info: writing psf file bubble.psf
total of 0 atoms
total of 0 bonds
total of 0 angles
total of 0 dihedrals
total of 0 impropers
Info: psf file complete.
Info: writing pdb file bubble.pdb
Info: pdb file complete.

But i have had other tcl scripts running in either of
above modes...I guess my script has to be modified.

regards
srinivasa
     
              ----x----
>Srinivasa,
> I didn't get anything in your last email, it was
>empty?

> John

 --- John Stone <johns_at_ks.uiuc.edu> wrote: >
> 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
> > > >
> > > > __________________________________
> > > > Do you Yahoo!?
> > > > Yahoo! SiteBuilder - Free, easy-to-use web
> site
> > > design software
> > > > http://sitebuilder.yahoo.com
> > >
> > > --
> > > 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
> >
> >
>
________________________________________________________________________
> > Yahoo! India Matrimony: Find your partner online.
> > Go to http://yahoo.shaadi.com
>
> --
> 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

________________________________________________________________________
Yahoo! India Matrimony: Find your partner online.
Go to http://yahoo.shaadi.com