VMD-L Mailing List

From: Ban Arn (ban.arn_at_gmail.com)
Date: Wed Feb 08 2012 - 15:59:22 CST

Dear John

I got the error in both windows & linux machine.

In windows I tried with VMD version 1.8.7 & in linux machine its VMD v 1.9.

Many Thanks
Balaji

On Wed, Feb 8, 2012 at 9:18 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Balaji,
> I just thought of something. Are you using a Windows machine to run
> these scripts, or are you using MacOS X or a Unix (e.g. Linux) machine?
> I ask because it is possible that if you're using Windows, one of the
> scripts
> may be incorrectly interpreting an end-of-file mark on a text file as an
> input character from the file. I'm going to ask someone here to run
> through
> the same tutorial on our machines to see if they encounter a problem like
> you're having or not.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 06, 2012 at 06:05:49PM +0000, Ban Arn wrote:
> > Dear Axel
> >
> > I'm following the vmd SMD tutorial
> > "
> http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/node6.html
> "
> >
> > The array "f" is defined in load-traj.tcl script.
> >
> > Many Thanks
> > Balaji
> >
> > On Mon, Feb 6, 2012 at 6:02 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >
> > On Mon, Feb 6, 2012 at 12:57 PM, Ban Arn <ban.arn_at_gmail.com> wrote:
> > > Dear Axel
> > >
> > > Initially load this trajectory file, then define dt as 1 and
> pulling
> > > velocity as 0.01 & Temperature (inclusing Boltzman constant) as
> 0.6
> > > and finally i'll use this script for calculating work done.
> >
> > i don't follow. where does the file come into play,
> > and where do you define the "f" array.
> >
> > i am no mind reader, so i cannot give advice
> > on stuff that i don't see.
> >
> > the error that you see, doesn't originate in the part of the code
> that
> > you quoted, but some *other* part, most likely where you define "f".
> > axel.
> > >
> > > Many Thanks
> > > Balaji
> > >
> > >
> > > On Mon, Feb 6, 2012 at 5:54 PM, Axel Kohlmeyer <
> akohlmey_at_gmail.com>
> > wrote:
> > >>
> > >> On Mon, Feb 6, 2012 at 12:51 PM, Ban Arn <ban.arn_at_gmail.com>
> wrote:
> > >> > Dear John & Axel
> > >> >
> > >> > Kindly find the attachment for reference file which I have been
> > using
> > >> > for
> > >> > the above script..
> > >> >
> > >> > The file has 11 columns 1st is time step, 2-6 columns are
> > displacement
> > >> > and
> > >> > 7-11 columns are respective forces.
> > >>
> > >> i don't see the relation of this file with the piece of script
> code.
> > >>
> > >> axel.
> > >>
> > >>
> > >> >
> > >> > Kindly advice.
> > >> >
> > >> > Many Thanks
> > >> > Balaji
> > >> >
> > >> >
> > >> >
> > >> > On Mon, Feb 6, 2012 at 5:46 PM, Axel Kohlmeyer <
> akohlmey_at_gmail.com>
> > >> > wrote:
> > >> >>
> > >> >> On Mon, Feb 6, 2012 at 11:50 AM, Ban Arn <ban.arn_at_gmail.com>
> > wrote:
> > >> >> > Dear VMD Users
> > >> >> >
> > >> >> > I'm using following script
> > >> >> >
> > >> >> > foreach l [array names f] {
> > >> >> > set w($l) {}
> > >> >> > set fsum 0
> > >> >> > foreach ftemp $f($l) {
> > >> >> > set fsum [expr $fsum + $ftemp * $v * $dt]
> > >> >> > lappend w($l) $fsum
> > >> >> > }
> > >> >> > }
> > >> >> >
> > >> >> > for the calculation of work done for 10 simulations.
> > >> >> >
> > >> >> > While running the script it shows error as "missing operand
> at
> > _@_
> > >> >> > in expression "0.25771 + _@_* 1 * 1"
> > >> >> >
> > >> >> > I'm not a tcl expert. Kinldy advice.
> > >> >>
> > >> >> ...and we don't know what you have in your "f" array.
> > >> >> apparently no numbers.
> > >> >>
> > >> >> axel.
> > >> >>
> > >> >>
> > >> >> >
> > >> >> > Many Thanks
> > >> >> > Balaji
> > >> >> >
> > >> >> >
> > >> >>
> > >> >>
> > >> >>
> > >> >> --
> > >> >> Dr. Axel Kohlmeyer
> > >> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> > >> >>
> > >> >> College of Science and Technology
> > >> >> Temple University, Philadelphia PA, USA.
> > >> >
> > >> >
> > >>
> > >>
> > >>
> > >> --
> > >> Dr. Axel Kohlmeyer
> > >> akohlmey_at_gmail.com http://goo.gl/1wk0
> > >>
> > >> College of Science and Technology
> > >> Temple University, Philadelphia PA, USA.
> > >
> > >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>