VMD-L Mailing List

From: ren (rsainiren_at_gmail.com)
Date: Wed May 09 2007 - 04:46:42 CDT

Sir,
I am new to the field of computational biology. I have just started being
familiar with the Linux OS. After searching I have found the following. Hope
this is the info required.
videosrc: v4lsrc; Driver : "vesa"
"Device"
    Identifier "Videocard0"
    Driver "vesa"
    VendorName "Videocard vendor"
    BoardName "VESA driver (generic)"

The VMD startup messages printed to the VMD text console:

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: 1561MB (77%)
Info) OpenGL renderer: Mesa GLX Indirect
Info) Features: STENCIL MDE MTX PP PS
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), Multitexture (8)
vmd > /usr/ren1/tutorial/TC5b_linear.pdb
invalid command name "/usr/ren1/tutorial/TC5b_linear.pdb"
vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
/usr/ren1/tutorial/TC5b
_linear.pdb: invalid ELF header
vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
/usr/ren1/tutorial/TC5b
_linear.pdb: invalid ELF header
vmd >

regards
Reena (rsaini)

On 5/9/07, ren <rsainiren_at_gmail.com> wrote:
>
> Sir,
> I am new to the field of computational biology. I have just started being
> familiar with the Linux OS. After searching I have found the following. Hope
> this is the info required.
> videosrc: v4lsrc; Driver : "vesa"
> The VMD startup messages printed to the VMD text console:
>
> 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: 1561MB (77%)
> Info) OpenGL renderer: Mesa GLX Indirect
> Info) Features: STENCIL MDE MTX PP PS
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), Multitexture (8)
> vmd > /usr/ren1/tutorial/TC5b_linear.pdb
> invalid command name "/usr/ren1/tutorial/TC5b_linear.pdb"
> vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
> /usr/ren1/tutorial/TC5b
> _linear.pdb: invalid ELF header
> vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
> /usr/ren1/tutorial/TC5b
> _linear.pdb: invalid ELF header
> vmd >
>
> regards
> Reena (rsaini)
>
> On 5/9/07, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> > Hi,
> > What video card and driver are you using? There's a
> > high probability that your video driver is the source of
> > this problem, so any information you have would be useful.
> > In particular, if you can send the VMD startup messages
> > printed to the VMD text console, that would be quite
> > helpful.
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, May 09, 2007 at 12:40:48PM +0530, ren wrote:
> > > Sir,
> > > I am using VMD 1.8.6 for Linux (32-bit x86) using OpenGL, downloaded
> > via
> > > your site: http://www.ks.uiuc.edu/Research/vmd/
> > > Though i am able to visualise the trajectory files from MD
> > simulations, I am
> > > unable to load any pdb file. As soon as I hit the load button to open
> > such
> > > file, the VMD window closes.
> > > I have even tried opening pdb file downloaded from www.rcsb.org but
> > > unsuccessful.
> > > when trying to open via command window it displays:
> > > vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> > > couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
> > > /usr/ren1/tutorial/TC5b_linear.pdb: invalid ELF header
> > > vmd >
> > > Need your help
> > > regards
> > > Reena( rsaini)
> >
> > --
> > 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
> >
>
>