VMD-L Mailing List

From: mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Fri Apr 22 2011 - 03:52:48 CDT

               Hi john,
                                I am using fitframes.tcl to fit the entire
protein ,to fis a particular residue let say 1 , what changes should i make
in the script.I am sending you the script , instead of all ,if i give resid
no its not working.

On Fri, Apr 22, 2011 at 9:23 AM, mohan maruthi sena
<maruthi.sena_at_gmail.com>wrote:

> 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
>>
>
>