VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 02 2009 - 10:39:18 CDT

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/      Fax: 217-244-6078