VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 21 2011 - 12:15:30 CDT

Hi,
  Try the version of the script I have attached to this email.
I found a number of problems in the version you just sent (some were
things that you had right in the first one, but got broken in the
most recent version).
This script should work better for you. Let me know if you still
get the convergence warnings. If so, it may be a good idea to add a
"puts" line in the fitting loop so you can determine what frames are
causing problems, and you can look at them more carefully to see what
the problem might be. My guess is that you're getting the warnings
because you have some large motions in the atom selection ("protein")
that prevent convergence. You may need to adjust the atom selection
and/or align separate components separately, if you have multiple subunits
in your simulation.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 21, 2011 at 10:19:02PM +0530, mohan maruthi sena wrote:
> 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 

-- 
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