VMD-L Mailing List

From: mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Thu Apr 21 2011 - 22:53:01 CDT

      I mean the error message is still same , even though we modified the
code.Protein selection is appropriate, it's working for other temperatures ,
only for some temperature dcd's it's giving this error message.

>
> When you say "not working" can you be more specific? Do you get
> the warnings still, or you have some other unrelated problem?
>
> Did you determine whether "protein" is an appropriate selection,
> and whether the warning occurs on specific frames or not?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Apr 22, 2011 at 12:24:04AM +0530, mohan maruthi sena wrote:
> > Sorry to say this is also not working john.
> >
> > On Thu, Apr 21, 2011 at 10:45 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> >
> > 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
>
> --
> 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
>