From: mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Thu Apr 21 2011 - 10:48:33 CDT

     Hi john i have run the script but its giving error as follows:

[: 338: i686: unexpected operator
[: 338: i686: unexpected operator
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
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, 2 CPUs detected.
Info) Free system memory: 752MB (75%)
Info) No CUDA accelerator devices available.
vmd -dispdev text < fit_frames.tcl -args psffile dcdfile temp_k
ionized.psf
md_300p_traj.dcd
300k
top
protein
Warning) Unable to ascertain filetype from filename 'psf'; assuming pdb.
ERROR) No molecules loaded.mol addfile operates on one molecule only
There is no 'top' molecule in atomselect's 'molId'
There is no 'top' molecule in atomselect's 'molId'
There is no 'top' molecule in atomselect's 'molId'
molinfo: get: no molecule exists with id -1
can't read "n": no such variable
can't read "n": no such variable
can't read "fin": no such variable
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) Exiting normally.

 With regards,
   Mohan.

On Thu, Apr 21, 2011 at 8:52 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> Before, looking into this further, the first thing I see that is a
> problem with your script is that you're using the old "mol load" command,
> and not forcing VMD to wait until the DCD file is completely loaded.
> I would suggest rewriting the script using the "mol new" and "mol addfile"
> commands ("mol load" will be removed from VMD soon), and add "waitfor all"
> to
> the end of the "mol new" and "mol addfile" commands to ensure that the
> trajectory is completely loaded before the script continues processing.
>
> The next question is which version of VMD you're using?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Apr 21, 2011 at 02:40:07PM +0530, mohan maruthi sena wrote:
> > Hi ,
> > I want to fit dcd from .dcd files of vmd and i have written a
> code
> > in tcl, actually its running well but for some files its giving error
> as
> > follows:
> > Matrix: Warning: no convergence (0.00000000<785.03826904 after 1000
> > iterations).
> [...]
> >
> > I am attaching the code ,please help me to fix this.
> >
> > Thanking you,
> > K.Mohan Maruthi
> > CCNSB,
> > IIIT-H
>
>
>
> --
> 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
>