VMD-L Mailing List

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Mon May 07 2012 - 15:54:51 CDT

I am using Quadro NVS 290.

Following is the start up message:

Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
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: 675MB (33%)
Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Gallium 0.4 on NV86
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
Info) File loading in progress, please wait.
Info) Using plugin pdb for structure file 3BDC.pdb
Info) Using plugin pdb for coordinates from file 3BDC.pdb
Info) Determining bond structure from distance search ...
Info) Eliminating bonds duplicated from existing structure...
Info) Finished with coordinate file 3BDC.pdb.
Info) Analyzing structure ...
Info) Atoms: 1179
Info) Bonds: 1100
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 237
Info) Waters: 106
Warning) Unusual bond between residues: 21 (protein) and 150 (none)
Warning) Unusual bond between residues: 40 (protein) and 150 (none)
Warning) Unusual bond between residues: 41 (protein) and 150 (none)
Warning) Unusual bond between residues: 43 (protein) and 150 (none)
Warning) Unusual bond between residues: 150 (none) and 157 (waters)
Warning) Unusual bond between residues: 150 (none) and 162 (waters)
Info) Segments: 1
Info) Fragments: 106 Protein: 1 Nucleic: 0

Thank you!

Wei Chen

On Mon, May 7, 2012 at 3:39 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> This sounds like a bug in your graphics driver.  What GPU are
> you using?  What startup messages are printed by VMD in the
> text console?
>
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Mon, May 07, 2012 at 03:17:21PM -0500, Wei Chen wrote:
>> Hi,
>>
>> When I draw a structure using 'Bonds' or 'Licorice' and color it by
>> 'Name', all bonds are shown as blue instead of different colors. This
>> happens for all versions of vmd I tried (1.9.1, 1.9, 1.8.6). I am
>> using a PC with Intel(R) Core(TM)2 Duo CPU. The operating system is
>> openSUSE 12.1 64bit. Any ideas about the problem?
>>
>> Thank you!
>>
>> Wei Chen
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078