VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Mar 15 2007 - 15:56:59 CDT

Hi,

In addition to what petter has said, perhaps you also saved the ions
included in your system (I assume there are a few of them). You could
try to select only the protein (for example, by using "atomselect top
protein").

Michel

2007/3/15, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> 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
> instead.
>
> Peter
>
> 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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