VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 06 2005 - 11:14:38 CDT

Hi,
  The PDB and PSF file formats were made by different people and do not
have the same limits on atom counts. (fun isn't it)
There's no standard way of having more than 99,999 atoms in a PDB file,
any software that supports such files is doing you a favor, since these
files technically violate the PDB specification. That said, most of the
popular MD packages will accept such files by virtue of ignoring the atom
index field completely, thus, it probably won't even matter.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 06, 2005 at 11:05:39AM -0500, Christina Payne wrote:
> I am trying to use the solvate plugin in VMD to add water to a very
> large system. I have successfully been able to solvate it as planned;
> however, in printing the pdb file with the water atoms tacked on the
> end, VMD prints ***** after 99999 atoms. Oddly enough, the
> corresponding psf file correctly numbers the atoms over 100000. Is
> there an option in solvate that would help me get around this, or do you
> think I will have to renumber them by writing my own program?
>
> Thanks,
> Christina Payne
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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