VMD-L Mailing List

From: Erkan Tuzel (tuzel_at_physics.umn.edu)
Date: Wed Jun 06 2007 - 19:39:48 CDT

Hi,

I have been using the XYZ file format for quite a while to display
atoms in a 2d plane. However, after I have upgraded the version
1.8.6, VMD gives the following
error while reading the data file:

Info) Using plugin xyz for structure file test.xyz
ERROR) BaseMolecule: Cannot add atom; namelist index value too large.
ERROR) Recompile VMD with larger index types.
ERROR) Atom namelist index values at time of overflow:
ERROR) nameindex: 111
ERROR) typeindex: 111
ERROR) resnameindex: 0
ERROR) segnameindex: 0
ERROR) altlocindex: 0
ERROR) chainindex: 0
ERROR) MolFilePlugin: file load aborted

Unless I reduce the number of atoms to the number specified, it does
not seem to work. I normally have around 2000-3000 atoms in a file
and the files work well with version 1.8.5. I use Mac OS X version
10.4 with PowerPC. Does anybody know a solution to this? Is this a
bug? 111 atoms seems to be pretty small.

Erkan