From: Paweł Kędzierski (
Date: Wed Sep 28 2011 - 08:17:35 CDT

The error cited indicates that exceeded is the capacity of a 16bit
integer variable used to index the /names/ of atoms.
Do you really need unique atom names for such a large system? It is
usually sufficient that the names are unique within residues.
If you can resign on unique atom names, then renaming them may be a much
simpler solution than recompilation of VMD, which is not a trivial task.
Pawel Kedzierski

W dniu 28.09.2011 07:50, JhonY. I. pisze:
> In win32 VMD, I've got the following error message.
> 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: 32768
> ERROR) typeindex: 0
> ERROR) resnameindex: 0
> ERROR) segnameindex: 0
> ERROR) altlocindex: 0
> ERROR) chainindex: 0
> ERROR) MolFilePlugin: file load aborted
> ERROR) molecule_structure: Unable to read structure for molecule 0
> ERROR) molecule_structure: severe error indicated by plugin aborting
> loading of
> molecule 0
> I've downloaded source files followng the message of "Recompile VMD
> with larger index types."
> However, I don't know what index I should change in the source files
> and how I compile the files in windows XP system.
> Would you let me know of them in detail or where I can get the guide
> file for it?
> Thanks for the helps in advance.
> Young