VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 02 2009 - 14:01:12 CDT

Lucie,
  After fixing an invalid filename for the .coor file (was looking
in a directory "'/media/disk/LUCIE/ionchannels/kv1/kv1.5/kv1.5.26/"
which obviously doesn't exist on my machine), the state file
you provided loads fine for me with both VMD 1.8.7 beta 5 and VMD 1.8.6.
If you run VMD 1.8.7 beta 5 and load the saved state via the command
line -e flag, how far does it get? Can you mail me the output from
that test? (no -debug)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 02, 2009 at 06:42:38PM +0200, lucie delemotte wrote:
> Hi,
> I uploaded the files to biocore (called state.tar.gz).
> Thanks again.
>
> Lucie
>
> On Tue, Jun 2, 2009 at 6:15 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > Can you tar up the saved state and related files, gzip it, and
> > either post it on biocore or email it to me (if it is small enough)?
> > I'd like to try loading it for myself so I can see what's going on there.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Jun 02, 2009 at 05:48:19PM +0200, lucie delemotte wrote:
> > > Thanks for the quick answer!
> > > Yes, vmd works fine when not loading a script (all windows open and I can
> > > load things from the graphical menu).
> > > Secondly, the script is supposed to load a pdb file plus a namdbin file.
> > > (With the other computer or in the debug mode, I get the same text as
> > above
> > > plus :
> > >
> > > Info) Using plugin pdb for coordinates from file
> > > kv1.5.26.0.pdb
> > > Info) Finished with coordinate file
> > > kv1.5.26.0.pdb.
> > > 0
> > >
> > > Info) Using plugin namdbin for coordinates from file ...
> > > ..........
> > > ........
> > > ........
> > > ........
> > > [New Thread 0xa8914b90 (LWP
> > > 25252)]
> > > [Thread 0xa8914b90 (LWP 25252)
> > > exited]
> > > [New Thread 0xa8113b90 (LWP
> > > 25253)]
> > > [Thread 0xa8113b90 (LWP 25253)
> > > exited]
> > > [New Thread 0xa8113b90 (LWP
> > > 25254)]
> > > [Thread 0xa8113b90 (LWP 25254)
> > > exited]
> > > [New Thread 0xa8914b90 (LWP
> > > 25255)]
> > > [Thread 0xa8914b90 (LWP 25255)
> > > exited]
> > > [New Thread 0xa8914b90 (LWP
> > > 25256)]
> > > [New Thread 0xa8113b90 (LWP
> > > 25257)]
> > > [Thread 0xa8914b90 (LWP 25256)
> > > exited]
> > > [Thread 0xa8113b90 (LWP 25257)
> > > exited]
> > > {{1 0 0 0.654825} {0 1 0 -0.0264271} {0 0 1 -9.97098} {0 0 0 1}}
> > {{-0.728706
> > > -0.681299 -0.0693803 0} {-0.060971 -0.0363649 0.997481 0} {-0.682102
> > > 0.731099 -0.01504 0} {0 0 0 1}} {{0.0266042 0 0 0} {0 0.0266042 0 0} {0 0
> > > 0.0266042 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0
> > > 1}}
> > > 0
> > >
> > > 0
> > >
> > > [New Thread 0xa8113b90 (LWP
> > > 25258)]
> > > [New Thread 0xa8914b90 (LWP
> > > 25259)]
> > > [Thread 0xa8914b90 (LWP 25259)
> > > exited]
> > > [Thread 0xa8113b90 (LWP 25258)
> > > exited]
> > >
> > > vmd >
> > >
> > >
> > > and the graphical window works fine.
> > >
> > > Lucie
> > >
> > >
> > >
> > > On Tue, Jun 2, 2009 at 5:39 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > > >
> > > > Hi,
> > > > Does VMD run correctly for you by itself? The main menu should
> > > > appear if it was installed correctly and you don't have an empty .vmdrc
> > > > in your home directory. Once you've verified that VMD itself is
> > working
> > > > fine, the next question I'd ask is whether you're loading any
> > coordinates
> > > > with that PSF file or just the PSF file. Unless you load coordinates
> > as
> > > > well, nothing will be displayed in the VMD graphics window. VMD needs
> > > > the atomic coordinates to be able to draw anything. The PSF file only
> > > > contains the structure data (e.g. bonds/angles/dihedrals/etc). When
> > you
> > > > loaded it in VMD 1.8.6, did the saved state also load a PDB file or
> > some
> > > > other coordinate file, or not?
> > > >
> > > > Cheers,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Tue, Jun 02, 2009 at 05:31:26PM +0200, lucie delemotte wrote:
> > > > > Hi all,
> > > > >
> > > > > I have a vmd state script (state.vmd) that was working properly with
> > vmd
> > > > > 1.8.6.
> > > > > After upgrading from mandriva 2008.0 to mandriva 2009.1 and changing
> > to
> > > > vmd
> > > > > 1.8.7, the script stopped loading (either in command line with vmd -e
> > > > > state.vmd or in the Tkconsole with the play command). The openGL
> > window
> > > > pops
> > > > > up but nothing appears in it while the vmd main window doesn't open.
> > In
> > > > the
> > > > > console, the regular vmd stuff appears :
> > > > >
> > > > > Info) VMD for LINUX, version 1.8.7beta5 (June 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: 326MB (16%)
> > > > >
> > > > > Info) No CUDA accelerator devices available.
> > > > >
> > > > > Info) OpenGL renderer: Quadro FX 3450/4000 SDI/PCI/SSE2
> > > > >
> > > > > Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVF)
> > > > >
> > > > > Info) Full GLSL rendering mode is available.
> > > > >
> > > > > Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture
> > (4)
> > > > >
> > > > > psfplugin) Detected a Charmm31 PSF file
> > > > >
> > > > > Info) Using plugin psf for structure file kv1.5.26.0.psf
> > > > >
> > > > > Info) Analyzing structure ...
> > > > >
> > > > > Info) Atoms: 305464
> > > > >
> > > > > Info) Bonds: 221738
> > > > >
> > > > > Info) Angles: 172116 Dihedrals: 117638 Impropers: 4748
> > Cross-terms:
> > > > > 1552
> > > > > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0
> > Impropertypes:
> > > > > 0
> > > > > Info) Residues:
> > > > > 85614
> > > > > Info) Waters:
> > > > > 83392
> > > > > Info) Segments:
> > > > > 21
> > > > > Info) Fragments: 84058 Protein: 4 Nucleic:
> > > > > 0
> > > > >
> > > > >
> > > > > I tested versions beta.2, beta.3 and beta.5 unsuccessfully. I also
> > > > checked
> > > > > that the script is still working on another computer. It also appears
> > > > that
> > > > > vmd 1.8.6 is not working at all (vmd main window not appearing) on
> > the
> > > > new
> > > > > installation.
> > > > > The Nvidia drivers are well installed with the latest version :
> > 180.51
> > > > > Tcl/Tk version 8.6
> > > > > gcc (GCC) 4.3.2
> > > > >
> > > > > I tried the debug mode to check what was wrong and interstingly, my
> > > > > state.vmd file loads properly (gdb version : 6.8-6mdv2009.1).
> > > > >
> > > > > Any help would be greatly appreciated.
> > > > > Lucie
> > > >
> > > > --
> > > > 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/><
> > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > 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