VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 13 2006 - 15:58:49 CDT

Gustavo,
  If you want an exact quantile then you'll have to calculate the distances
for the candidates your interested in, sort them, and select the N you care
about. In VMD you'd do something like:
  1) select all waters within the max cutoff distance M
  2) calculate the distance D of each water molecule and add the index and
     distance to a list or lists
  3) sort the list(s) by the distance (keeping the water index and distance
     assocation intact, if they are in separate lists..)
  4) select the closest N waters from the sorted list

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 13, 2006 at 01:39:31PM -0400, Gustavo Seabra wrote:
> Hi,
>
> I have a system of a small peptide in explicit water. I know, for
> example, how to select all waters within a certain distance of the
> peptide.
>
> Now, what I'd like to do instead is to select the 'N' waters closest
> to the peptide. Is that possible? I looked into the VMD manual and
> couldn't find anything. Maybe some script?
>
> Thanks a lot!
>
> Gustavo. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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