VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 24 2006 - 13:11:11 CDT

Hi,
  Regarding your simulation question, I think you'll get a better response
by asking this to namd-l_at_ks.uiuc.edu which is the mailing list for NAMD.
Regarding making changes to your PDB file, I assume that what you need to do
there is set the "beta" or "occupancy" column with one or zero? If so,
then you can do something like this (I made up an arbitrary "forcesel"
selection, you'll have to use the right selection(s) for your specific case):
  mol new original.pdb
  set allsel [atomselect top "all"]
  $allsel set beta 0

  set forcesel [atomselect top "not water"]
  $forcesel set beta 1

  $allsel writepdb forces.pdb

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 24, 2006 at 11:41:54AM -0500, Al-Rawi, Ahlam wrote:
> Dear All,
> I have a system of water and beta-sheet.
> I need to know how I can apply external force that seperate the two part of the beta sheet in the water.
> I look at the documents on line. What I understand that I need to add the changes to the pdb file, how I can do that.
> Thanks for your help
> Ahlam
>
> Ahlam Al-Rawi
> Physics Department
> Kansas State University
> 785-532-5520
> cell 785-317-5858
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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