VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 11:07:27 CDT

Ajasja,
  I have worked through debugging this, and it looks to me like the
DCD file produced by Vega ZZ is incorrectly formatted. At the point in
the file where the NTITLE data that specifies the number of TITLE lines
should be, there is a HUGE number, 1095062083, which is obviously incorrect.

Either Vega ZZ is outputting the NTITLE data incorrectly, or something has
gone wrong in its DCD output in the records that precede the NTITLE data,
leading to this problem. The fortran record size data that immediately
precedes the NTITLE data seemed to be correct, so it looks to me like
it's just outputting bad data for the NTITLE value. I would suggest that
you contact the Vega ZZ authors about this, and see if you can load this
DCD file into CHARMM. My assumption is that you will not be able to load it
into CHARMM either.

The VMD DCD plugin is actually pretty liberal about accepting
numerous variations of DCD files, but this one already has some
bad data in the DCD header itself, making it hard to work around.

I have already tried changing the DCD plugin so that it detects this case
and tries to soldier on, but the data that follows the NTITLE word also
seems out of place even if I tell the VMD DCD plugin to skip past the
troubled NTITLE block.

I'll spend a short time more looking at this to see if I can give you
more concrete suggestions to send to the Vega ZZ authors, but this is
clearly a mis-formatted DCD file.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 19, 2010 at 10:39:50AM -0500, John Stone wrote:
>
> Hi,
> Something is fishy with the DCD file produced by Vega ZZ, it is
> triggering a type of error handling loop in the VMD DCD plugin repeatedly
> trying to do a seek. I will have to debug this carefully and get back to you.
>
> Cheers,
> John
>
> On Tue, Oct 19, 2010 at 04:21:44PM +0200, Ajasja Ljubeti?? wrote:
> > Dear All,
> > I wanted to perform a conformational search on a spin label. The simplest
> > way seemed to me, to use Vega ZZ to generate a trajectory of different
> > rotamers and analyze the results using VMD/NAMD. But if I try to open the
> > trajectory file then VMD stops responding. The CPU goes to max (for one
> > thread) and nothing much happens, although in this test trajectory there
> > are only 6 frames. I have tried manually setting first and last frame but
> > that didn't help. Any suggestions?
> > Best regards,
> > Ajasja
> > Info) VMD for WIN32, 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, 4 CPUs detected.
> > Info) Free system memory: 4095MB (100%)
> > Info) Detected 1 available CUDA accelerator:
> > Info) [0] GeForce GTS 250 16 SM_1.1 @ 1.85 GHz, 1005MB RAM, OIO
> > Info) Creating CUDA device pool and initializing hardware...
> > Info) OpenGL renderer: GeForce GTS 250/PCI/SSE2
> > Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> > Info) No joysticks found. Joystick interface disabled.
> > Info) Using plugin psf for ***
> > psfplugin) no cross-terms defined in PSF file.
> > Info) Analyzing structure ...
> > Info) Atoms: 40
> > Info) Bonds: 40
> > Info) Angles: 74 Dihedrals: 101 Impropers: 12 Cross-terms: 0
> > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > Info) Residues: 1
> > Info) Waters: 0
> > Info) Segments: 1
> > Info) Fragments: 1 Protein: 1 Nucleic: 0
> > dcdplugin) detected standard 32-bit DCD file of native endianness
> > dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
>
>
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ 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
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078