VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 18 2007 - 16:04:51 CDT

Hi,
  Judging by the behavior you're observing, the system hang indicates
either a bad kernel, or a bad video driver. Since your email doesn't
indicate what video card or driver you're using, it's hard for me to
judge specifically. Those are the two most likely candidates leading
to your problem. Since the system hang occurs when you change the
graphical representation, I wonder if it might be a problem with the
video card or video driver. If you tell me more about your system,
I may have further suggestions.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 18, 2007 at 10:29:06AM +0530, Vijaya Brahma wrote:
> Sir
> With due respect i want to state the problem that I am facing while
> running VMD 1.8.6 for Linux (32-bit x86) using OpenGL, downloaded via
> http://www.ks.uiuc.edu/Research/vmd/
> The problem is that I am unable to load a PDB file, as soon I load a PDB
> file the VMD crashes. I have tried to debug and run, using following
> command
> vmd -debug
> (gdb) run
> as a consequence I am able to load the PDB file but when I try to change
> the graphical representation of the molecule, the system hangs:-
> these are the steps that occured in the terminal,
>
> vmd > mol new /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb
> Info) Using plugin pdb for structure file
> /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb
> Info) Using plugin pdb for coordinates from file
> /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb
> Info) Determining bond structure from distance search ...
> Info) Eliminating bonds duplicated from existing structure...
> [New Thread 45882288 (LWP 29963)]
> [Thread 45882288 (LWP 29963) exited]
> [New Thread 62696368 (LWP 29964)]
> [Thread 62696368 (LWP 29964) exited]
> Info) Analyzing structure ...
> Info) Atoms: 4604
> Info) Bonds: 4709
> Info) Residues: 604
> Info) Waters: 15
> Info) Segments: 1
> Info) Fragments: 19 Protein: 4 Nucleic: 0
> 0
> Info) Finished with coordinate file
> /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb.
> vmd > Info) In any publication of scientific results based in part or
> Info) completely on the use of the program STRIDE, please reference:
> Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
> Detaching after fork from child process 29965.
> ptrace: No such process.
> [Switching to Thread 62696368 (LWP 29964)]
> Cannot remove breakpoints because program is no longer writable.
> It might be running in another process.
> Further execution is probably impossible.
> 0x080f8fbc in BaseMolecule::~BaseMolecule$delete ()
> (gdb)
>
> Kindly help,
>
> THanking You,
>
> Regards
> --
> ...................................................................
> VIJAYA BRAHMA
> ..................................................................
> Research Scholar
> Protein Science & Engineering
> Institute of Microbial Technology(IMTECH)
> Chandigarh
> India
> http://www.imtech.res.in/bic/phd.html 

-- 
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