VMD-L Mailing List

From: Nicholas Musolino (musolino_at_mit.edu)
Date: Fri Jun 18 2010 - 08:40:44 CDT

Dear Balaji,

How would you define "involved in hydrophobic interaction with ligand"? If you're able to define this question precisely in terms of the coordinates of all the atoms of your system, you will be able to calculate the list in VMD.

For example, you might define the criteria as follows: a residue is involved in a hydrophobic interaction with a ligand where:
(a) the residue is of the residues commonly thought of as hydrophobic, namely I, L, M, F, W, Y, and maybe A, AND
(b) the center of mass of the residue is within 6 A of the center of mass of the ligand (or something like this).

Or you could revise the criterion (b) to be based on distances of certain atoms, or some distance plus some angle, etc. This definition of a hydrophobic interaction is not trivial and is the key question.

Once you have this in mind, see the Scripting tutorial and the documentation for the atomselect command:
http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node107.html

You may have to learn a little of the TCL-based scripting language, but there are many examples out there and I think you'll find VMD very helpful.

Best of luck!

Nicholas

---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528

On Jun 18, 2010, at 6:59 AM, ban arn wrote:

> Dear All
>
> I am intrested in calculating the list of residues involved in hydrobhoic interaction with ligand over my trajectories. Is it possible in VMD.
>
> Kindly advice.
>
> Many Thanks
> Balaji