From: John Stone (
Date: Wed Mar 24 2004 - 16:01:07 CST

  Assuming that your ions are named in an identifiable manner,
you ought to be able to write a script that uses atom selections similar to:
  "name foo and within 10 of (resid blah or resid blah2 or resid blah3)"

You'd then write the script so that you'd do that selection for all frames,
updating a "bin" for each atom index when its near your areas of interest.
You can get an idea of how to do this sort of thing by looking at a
recently posted script that does something similar for a different problem
("Re: density profile"):

Once you've cruised through all of the frames in the trajectory you'll
have a count of the number of trajectory timesteps that a given ion was
within one of your areas of interest.

My description is a crude first approximation but should be easy for you
to write if you know what you want out of it.

  John Stone

On Tue, Mar 23, 2004 at 07:51:10PM -0800, Ioana Cozmuta wrote:
> Hello,
> Is there a standard procedure to calculate residence times of ions around
> certain amino acids from MD trajectories? Does anyone have a script
> already written to do that? Or is it up to each individual how to define
> and calculate such a quantity?
> Thank you,
> Ioana
> ******************
> Ioana Cozmuta, PhD
> Research Scientist Eloret Corporation
> Mail Stop 230-3
> NASA AMES Research Center
> Moffet Field, CA 94035-1000
> Phone: (650) 604-0993

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:                 Phone: 217-244-3349              
  WWW:      Fax: 217-244-6078