VMD-L Mailing List

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Tue Apr 20 2004 - 04:19:14 CDT

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
_@_"