VMD-L Mailing List

From: lucie delemotte (lucie.delemotte_at_edam.uhp-nancy.fr)
Date: Tue Jun 02 2009 - 10:48:19 CDT

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 ...
..........
........
........
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{{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

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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
>