From: mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Thu Apr 21 2011 - 11:49:02 CDT

        Hi john ,
                      Please find the attached script.I have one doubt if
script is wrong it should give errors to all the fit dcds, but it is giving
error only at some particular temperatures.
On Thu, Apr 21, 2011 at 9:47 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
>