VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 02 2009 - 11:15:39 CDT

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/      Fax: 217-244-6078