From: Peter Freddolino (
Date: Thu Mar 15 2007 - 15:29:05 CDT

Hi Lily,
autopsf will fill in any missing atoms in residues, so if you
accidentally cut out some solute atoms when removing the water, or are
missing termini, these will be added. If you send your files I can track
down the specific differences (you can probably do the same by looking
at what atoms are present only in one).
Are you planning to use this psf for visualization or energetic
analysis? If you only need it for visualization, you can just use a pdb


lily jin wrote:
> Hi,
> My protein was in a waterbox during simulation. I want to removed the
> waterbox when I analyze the results. I saved a dcd file without water.
> The atom number is 51353. Then I use AutoPSF plugin to generate a PSF
> file without water. However, the genrated PSF and PDB files include
> 51380 atoms. What makes the difference? What can I do to make them
> match? Thank you!
> *Lily*
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