VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 20 2010 - 16:37:47 CDT

Hi,
  As I described before, the .coor files don't contain occupancy
data at all, so the only way those values would be getting set to
a value other than zero would be either by loading a pdb or other
file that contains occupancy data, by setting it with an atom selection,
or due to a previously unknown bug of some kind.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 20, 2010 at 11:35:35AM -0400, Parisa Akhski wrote:
> Hi John,
>
> Thanks for your reply. You are right, when I load both psf and original
> pdb files along with .coor and save .coor as pdb file, the occupancy in
> the generated pdb file is 1.00 for all atoms which is good. But, if I just
> use psf and .coor files to load and save as pdb, it's kind of random.
> Sometimes (for some DNA sequences and for some MS simulation steps) it
> produces 1.00 as occupancy and sometimes 0.00 for all atoms. I don't
> understand this. To the best of my knowledge, occupancy estimates the
> amount of each conformation that is observed in the structure and my
> original structure has just one conformation so I expect my pdb file to
> show this number always 1.00 for all atoms.
> BTW, I finished the simulation which has several steps. In some steps I
> constrained part of the structure and ran the simulation and then I used
> the generated .coor file at each step to move on the next one (restart
> job). Since some of the .coor files in these series of simulations
> included 0.00 for occupancy, is the final result reliable?
> Obviously, to restart each job (moving to the next step) I am using a pdb
> file (which has occupancy 1.00) in addition to the psf and .coor (from the
> previous step). So, I assume the final results shouldn't be affected too
> much or even at all.
> Please reply me if you have any idea in this case since it took me almost
> 1 month to finish this job and I want to know whether I can use the
> results.
>
> Thanks,
> Parisa
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Sun 9/19/2010 3:09 PM
> To: Parisa Akhski
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: minimization changed the occupancy of all atoms to
> zero
>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078