VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Sep 19 2010 - 14:09:41 CDT

Hi,
  i think the issue there is that the .coor file doesn't contain
occupancy information, thus it goes to all zeros if you load it without
the original PDB file.

Cheers,
  John

On Fri, Sep 17, 2010 at 05:17:11PM -0400, Parisa Akhski wrote:
> Dear all,
>
> In minimization of a DNA system, I started with a pdb file with the
> occupancy value equal to 1.0 for all atoms. However, the coordinate file
> (.coor) produced after minimization gives the occupancy equal to zero for
> all atoms. Does anyone have any idea why this happens? Is it OK to
> continue MD simulation with this output file?
>
> Thanks,
> Parisa 

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