VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 20 2004 - 09:37:19 CDT

Lubos,
  Wow, that's interesting. By the way, from what youv've sent below,
I'd strongly recommend that you upgrade to VMD 1.8.2. The version you're
running isn't even a proper release version of VMD, so there's no telling
what bugs are in that alpha code that we've long since fixed..

Since the core file is large, do this and email me the results:
  gdb /usr/local/lib/vmd_LINUX vmd_LINUX.core

Once loaded, type the command "where" and email me what it says.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 20, 2004 at 11:19:14AM +0200, Lubos Vrbka wrote:
> hi,
>
> > You used the word "crash", but it sounds like the plugin is just
> >returning an error message, is this correct? Lets only use the word
> >"crash" to refer to actual program crashes, so as not to cause confusion.
> >:-)
> no, i meant crash, it crashes with coredump:
>
> Info) VMD for LINUX, version 1.8.1a6 (March 25, 2003)
> 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, 1 CPU detected.
> Info) OpenGL renderer: Mesa X11
> Info) Features: STENCIL RN CVA MTX
> Info) Textures: 2-D (2048x2048), 3-D (2048x2048x2048), Multitexture (2)
> Unable to dlopen
> '/usr/local/lib/vmd_alpha/plugins/LINUX/molfile/webpdbplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd_alpha/plugins/LINUX/molfile/webpdbplugin.so
> xyz) trying to open file 'traj.xyz'
> Info) Using plugin xyz for structure file traj.xyz
>
> xyz) trying to read structure and coordinates of 220 atoms.
> Info) Determining bond structure from distance search ...
> ERROR) MolAtom 23: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 30: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 11: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 33: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 10: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 18: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 25: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 27: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 13: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 29: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 36: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 26: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 28: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 39: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 8: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 38: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 14: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 19: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 37: Exceeded maximum number of bonds (8).
> Info) Analyzing structure ...
> Info) Atoms: 220
> Info) Residues: 26
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 26 Protein: 0 Nucleic: 0
>
> xyz) ERROR: expecting 220 atoms, found only 221.
> xyz) trying to close file 'traj.xyz'
> Info) Finished with coordinate file traj.xyz.
> Segmentation fault (core dumped)
>
> if the vmd_LINUX.core file is of some interest for you let me know and
> we can decide how to transfer it to you (as it has ~18mb and probably
> wouldn't pass through any mailserver)...
>
> regards,
>
> --
> Lubos
> _@_" 

-- 
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