VMD-L Mailing List

From: Vijaya Brahma (vbrahma_at_imtech.res.in)
Date: Sun Jun 17 2007 - 23:59:06 CDT

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