VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Mon Sep 20 2010 - 10:35:35 CDT

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