VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 31 2012 - 11:57:29 CDT

Hi,
  If you can store your trajectory in a format VMD can read, you could
use the VMD atom selection mechanism to do the sort of calculations
you're asking about, by following the various VMD tutorial
atom selection and scripting examples. If you can't load your trajectory
directly into VMD, then you would also need to write the code to read in
the data for yourself, and do the spherical distance checks for yourself
rather than using atom selections.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 31, 2012 at 11:51:52AM +0000, Gamot, Ritchie wrote:
> Dear All,
>
> good day!
>
> i would like to be able to know how to go through all the atoms in my file
> and calculate the distance of it to allthe other atoms. like, get ARG1 and
> compute the distance to ARG2, ARG3, etc and possibly take the sum of in
> the end.
>
> i also would like to determine a sort of nearest neighbor cmputation. like
> for example, i take ARG1, i would like to determine the atoms/points which
> are in a distance of dist from it. so basically if i take a sphere around
> an atom/point, i would like to determine the atoms that are included in
> that sphere. i need to do this for each atom in my molecule.
>
> i do hope that you can help me out with this query of mine, as of now i am
> looking into several possible scripts that i can use from the uiuc website
> but hopefully if you can help me with this, i would appreciate it a lot.
>
> thank you very much!
>
> regards,
>
> Chimie Gamot
>
> i have a trajectory file in the format:
>
> 98
> Frame 0
> ARG1 1.23 0.79 0.45
> ARG2 2.90 -1.23 0.004
> .
> .
> ARG98 1.56 -1.43 0.89
> 98
> Frame 1
> ARG1 0.23 2.79 -0.45
> ARG2 -1.90 -2.23 3.004
> .
> .
> ARG98 1.43 -1.27 0.12
> etc
> etc
> etc
>
> and i have another reference file of the format:
>
> 98
> Reference
> ARG1 2.23 1.79 -0.45
> ARG2 -1.90 2.23 1.004
> .
> .
> ARG98 1.34 -2.43 1.29 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078