VMD-L Mailing List

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Jul 13 2006 - 16:39:59 CDT

Thanks John,

I can see how to build the algorithm. However, I don;t have any
experience coding for VMD. Could you tell me where I can read some
material about it, so I can try to start coding that?

Thanks,

Gustavo.

On 7/13/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
> 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