VMD-L Mailing List

From: lucie delemotte (lucie.delemotte_at_edam.uhp-nancy.fr)
Date: Wed Jun 03 2009 - 02:36:51 CDT

Hi,

I tried what you suggested and the output is the following :

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: 561MB (27%)
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
0
Info) Using plugin pdb for coordinates from file kv1.5.26.0.pdb
Info) Finished with coordinate file kv1.5.26.0.pdb.

After that, I get no vmd> prompt. The openGL window opens but doesn't show
anything and no main window appears. I then have to kill the process to
quit.
I also forgot to mention that every script I have works well in the -dispdev
text mode.

Cheers again,
Lucie

On Tue, Jun 2, 2009 at 9:01 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/><
> > > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>