VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 10 2005 - 10:30:20 CDT

Hi,
  You can use scripting to get a list of each of the residues that are
involved in the contacts you're interested in. From there, you can
easily create atom selections for each residue and measure the center
of mass for that selected residue. A crude script that would do something
like this would look roughly like (I'm just doing lipids only):
  set mysel [atomselect top "lipid within 3 of protein"]
  set residuelist [lsort -unique [$mysel get residue]]
  puts "list of residues within 3 of protein:"
  puts "$residuelist"
  foreach res $residuelist {
    set rsel [atomselect top "residue $res"]
    set com [measure center $rsel weight [$rsel get mass]]
    puts "Residue: $res COM: $com"
    $rsel delete
  }

You can do the same thing to get the list of protein residues etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 10, 2005 at 01:13:39PM +0100, syma wrote:
> Hi,
>
> I am (still) trying to get detailed information regarding protein-lipid
> contacts. I would like to use the 'within' and 'measure' commands to get
> information on all protein-lipid contacts within eg 3 angstroms of each
> other. I would also like to get the coordinates of the centre of mass of the
> protein and lipids that are involved in each contact.
>
> I would very much appreciate some assistance with this.
>
> Best wishes,
>
> -Syma
>
> ***************************************************
>
> Dr Syma Khalid
> Department of Biochemistry,
> University of Oxford
> South Parks Road,
> Oxford
> OX1 3QU
> U.K.
>
>
>
> ***************************************************
>
> 

-- 
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