VMD-L Mailing List

From: Vijaya Brahma (vbrahma_at_imtech.res.in)
Date: Wed Jun 20 2007 - 23:31:27 CDT

Sir,

Regarding the previous mail dealing with the problem of inability to load
graphical represenation in VMD 1.8.6 for Linux (32-bit x86) using OpenGL
I am hereby mentioning the specifications of my system:-

linux Distribution version
Linux version 2.6.9-5.ELsmp (bhcompile_at_decompose.build.redhat.com)
(gcc version 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)) #1 SMP

kernel:
Linux 2.6.9-5.ELsmp #1 SMP
 i686 i686 i386 GNU/Linux

CPU type:
i686

CPU model:
model name : Intel(R) Pentium(R) 4 CPU 3.60GHz

libc version:
libtermcap.so.2 => /lib/libtermcap.so.2 (0x00b36000)
        libdl.so.2 => /lib/libdl.so.2 (0x00928000)
        libc.so.6 => /lib/tls/libc.so.6 (0x007d8000)
        /lib/ld-linux.so.2 (0x007bb000)

video card:
VESA driver generic

Video Driver:
server glx vendor string: SGI
server glx version string: 1.2
client glx vendor string: SGI
client glx version string: 1.4
OpenGL vendor string: Mesa project: www.mesa3d.org
OpenGL renderer string: Mesa GLX Indirect
OpenGL version string: 1.2 (1.5 Mesa 6.1)

I was wondering if there is problem is in VMD finding the Mesa/OpenGL
shared libraries,the command
vmd -dispdev text
confirmed that the problem does not lie there as it started
normally,showing absolutely no error . The result was as follows :-
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: 612MB (60%)
vmd >

Kindly help

Regards, 

-- 
....................................................................
VIJAYA BRAHMA
...................................................................
Research Scholar
Protein Science & Engineering
Institute of Microbial Technology(IMTECH)
Chandigarh
India
http://www.imtech.res.in/bic/phd.html
>
> 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
>
>