From: John Stone (
Date: Tue Jan 24 2006 - 15:26:18 CST

  The PDB format doesn't allow more than 99,999 atoms due to the 5 character
atom index field width. As such, VMD and the various structure building
plugins built on top of it honor the field width limitation but stop emitting
valid index numbers since these are ignored by NAMD and several of the other
simulation packages anyway. Any package that accepts PDB files containing
more than 99,999 atoms has to be prepared for unusual content since this
exceeds the design of the file format.

  John Stone

On Tue, Jan 24, 2006 at 04:06:15PM -0500, Jindal Shah wrote:
> Hi,
> I would like to solvate a very large protein complex. The number of
> water molecules obtained by solvate package in VMD is more than 99,999. This
> causes ***** to be displayed in the index field. Is there a work around
> for this type of problem? How do I write pdb files using solvate that
> contains more than 99,999 atoms?
> Thanks

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