VMD-L Mailing List

From: Roland Schmucki (schmucki_at_gsc.riken.jp)
Date: Thu Sep 13 2007 - 03:32:05 CDT

Hello!

To get to know the features of VMD, I am studying the "VMD Images and
Movies Tutorial".
http://www.ks.uiuc.edu/Training/Tutorials/vmd-ref/imgmv/tutorial-html/node3.html
However, in the second unit, "Working With Trajectories", I couldn't
load the dna.psf and trajectory.dcd files correctly. When loading
(file->new molecule->filename:dna.psf etc), none of the molecules was
displayed, although no error in the VMD console window was shown (see
below). I've tried that on a linux and windows workstation, but it
didn't work neither of them. So, there's something I did the wrong way.

Thank you for any help and suggestions!

Roland

Here is the "vmd console"-output:

Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
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: 1107MB (54%)
Info) OpenGL renderer: GeForce FX 5500/AGP/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX PP PS GLSL(OVF)
Info) OpenGL shader linkage log:
Info) Fragment info
Info) -------------
Info) <stdlib>(6994) : error C5108: unknown semantics "FACE" specified
for "gl_FrontFacing"
Info) (65) : warning C7050: "texcolor" might be used before being
initialized
Warning) GPU driver failed to compile shader:
Warning) /home/roland/VMD/LIB/shaders/vmd
Warning) This GPU/driver is buggy, or doesn't fully implement GLSL.
Warning) Set environment variable VMDGLSLVERBOSE for more info.
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
/home/roland/.mozilla/firefox2/firefox -remote openURL(%s)
/home/roland/.mozilla/firefox2/firefox %s SPMamp &1
vmd > Info) Using plugin psf for structure file
/home/roland/VMD/Tutorial/imgmv-tutorial-files/dna.psf
Info) Analyzing structure ...
Info) Atoms: 23217
Info) Bonds: 15417
Info) Residues: 7833
Info) Waters: 7532
Info) Segments: 5
Info) Fragments: 7823 Protein: 0 Nucleic: 1
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file
/home/roland/VMD/Tutorial/imgmv-tutorial-files/trajectory.dcd
Info) Finished with coordinate file
/home/roland/VMD/Tutorial/imgmv-tutorial-files/trajectory.dcd.