VMD-L Mailing List

From: mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Thu Apr 21 2011 - 13:54:04 CDT

         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
>