From: Axel Kohlmeyer (
Date: Wed Jun 06 2007 - 19:00:56 CDT

On Wed, 6 Jun 2007, Erkan Tuzel wrote:

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

ET> error while reading the data file:
ET> Info) Using plugin xyz for structure file
ET> ERROR) BaseMolecule: Cannot add atom; namelist index value too large.
ET> ERROR) Recompile VMD with larger index types.
ET> ERROR) Atom namelist index values at time of overflow:
ET> ERROR) nameindex: 111
ET> ERROR) typeindex: 111

try giving all atoms the same name.


ET> ERROR) resnameindex: 0
ET> ERROR) segnameindex: 0
ET> ERROR) altlocindex: 0
ET> ERROR) chainindex: 0
ET> ERROR) MolFilePlugin: file load aborted
ET> Unless I reduce the number of atoms to the number specified, it does
ET> not seem to work. I normally have around 2000-3000 atoms in a file
ET> and the files work well with version 1.8.5. I use Mac OS X version
ET> 10.4 with PowerPC. Does anybody know a solution to this? Is this a
ET> bug? 111 atoms seems to be pretty small.
ET> Erkan

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.