VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 21 2011 - 11:17:02 CDT

Hi,
  Send me your script, you undoubtably have a syntax error in your
use of "mol new", as it isn't the same syntax as the old "mol load"
command...

Cheers,
  John

On Thu, Apr 21, 2011 at 09:18:33PM +0530, mohan maruthi sena wrote:
> 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 

-- 
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